Diff of the two buildlogs: -- --- b1/build.log 2024-05-14 18:35:11.752007762 +0000 +++ b2/build.log 2024-05-14 19:03:50.002882465 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 14 06:19:48 -12 2024 -I: pbuilder-time-stamp: 1715710788 +I: Current time: Tue Jun 17 14:58:19 +14 2025 +I: pbuilder-time-stamp: 1750121899 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,51 +33,83 @@ dpkg-source: info: applying skip-dssp-tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1270620/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 17 00:58 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8747966a3bda428bb2a946bdd734f978' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1270620' - PS1='# ' - PS2='> ' + INVOCATION_ID=0d315648292d4426a203bc0cfc9d7c59 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=324423 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PQB1wPpT/pbuilderrc_J0J8 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PQB1wPpT/b1 --logfile b1/build.log openstructure_2.5.0-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PQB1wPpT/pbuilderrc_d2Bc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PQB1wPpT/b2 --logfile b2/build.log openstructure_2.5.0-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 14 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1270620/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 16 03:15 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -601,7 +633,7 @@ Get: 442 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.13.0-1+b1 [79.5 kB] Get: 443 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.10+dfsg-1+b1 [2501 kB] Get: 444 http://deb.debian.org/debian unstable/main amd64 voronota amd64 1.22.3149-2 [2057 kB] -Fetched 300 MB in 4s (71.2 MB/s) +Fetched 300 MB in 7s (40.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19700 files and directories currently installed.) @@ -2013,8 +2045,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue May 14 18:25:07 UTC 2024. -Universal Time is now: Tue May 14 18:25:07 UTC 2024. +Local time is now: Tue Jun 17 01:06:15 UTC 2025. +Universal Time is now: Tue Jun 17 01:06:15 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-2.1+b1) ... @@ -2414,7 +2446,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/openstructure-2.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../openstructure_2.5.0-2_source.changes +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/324423/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/openstructure-2.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../openstructure_2.5.0-2_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.5.0-2 dpkg-buildpackage: info: source distribution unstable @@ -2503,8 +2539,8 @@ Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF --- Configuring done (2.0s) --- Generating done (0.4s) +-- Configuring done (4.6s) +-- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: @@ -2528,1239 +2564,1224 @@ make[2]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend -make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend -make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend -make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" +make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake "--color=" +make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake "--color=" +make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake "--color=" +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake "--color=" make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend -make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake "--color=" -make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend +make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake "--color=" -make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend +make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake "--color=" -make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake "--color=" +make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py -make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build -make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py +make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py -make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build -make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/bin +make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py -make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build +make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib +make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/images/logo-small.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./cleanup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/bin +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/pymod/./cleanup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py -[ 0%] Built target ost_geom_pymod cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./lga.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py +make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tests +[ 0%] Built target ost_db_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 0%] Built target subst___init__.py +[ 0%] Built target ost_geom_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake "--color=" make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend +make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend +[ 0%] Built target gui_images make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py -[ 0%] Built target ost_gfx_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/tests -[ 0%] Built target ost_db_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py -[ 0%] Built target ost_conop_pymod -make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py -make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/io/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py +[ 0%] Built target ost_gfx_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./msms.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py +make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py -[ 0%] Built target gui_images +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake "--color=" +[ 0%] Built target ost_conop_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png +[ 0%] Built target create_stage make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./msms.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py -make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build +make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py -make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py -make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build +make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/init.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/distance_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py -[ 0%] Built target create_stage -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/custom_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py +make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake "--color=" -[ 0%] Built target ost_img_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./views.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/find_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py +[ 0%] Built target ost_img_alg_pymod +[ 0%] Built target ost_mol_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/custom_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py -[ 0%] Built target ost_info_pymod -[ 0%] Built target ost_mol_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./antechamber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py +[ 0%] Built target ost_img_pymod +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build -[ 0%] Built target ost_img_alg_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/information_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake "--color=" +[ 0%] Built target ost_info_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake "--color=" +[ 0%] Built target ost_gui_dng_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py +make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build -[ 0%] Built target ost_gui_dng_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" +[ 0%] Built target ost_io_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py +make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png -make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/pymod/./antechamber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" +make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py +[ 0%] Built target ost_mol_mm_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target ost_io_pymod -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/menubar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./trajectory_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py +[ 0%] Built target ost_seq_pymod +make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -[ 0%] Built target ost_seq_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target subst_ost_startup.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./trajectory_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py -make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py -[ 0%] Built target ost_mol_mm_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake "--color=" -[ 0%] Built target ost_gui_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./structure_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.5.0/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.9 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.5.0/cmake_support/substitute.cmake -make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py +make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-ligand-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py +[ 0%] Built target subst_ost_startup.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py [ 0%] Built target subst_ost_config -make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend +make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake "--color=" +make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-ligand-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-ligand-structures -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./structure_analysis.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh [ 0%] Built target subst_ost +make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./base.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./config.hh +[ 0%] Built target subst_dng +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./settings.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex1 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./def.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh -make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh -[ 0%] Built target subst_dng -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./lddt.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./lddt.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/actions/ost-compare-structures-legacy /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures-legacy -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py -make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh +[ 0%] Built target ost_gui_pymod cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./exc.hh +make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/site_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dllexport.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./lddt.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./lddt.py +make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscore.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./geom.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./version.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./version.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/test_utils/compare_files.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./scoring.py [ 0%] Built target actions make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/config/./version.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./version.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./qsscore.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscore.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./table_selector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./chain_mapping.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./chain_mapping.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./generic_property.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./scoring.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py -[ 0%] Built target ost_seq_alg_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png [ 0%] Built target ost_config_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake "--color=" -make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat2.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./stereochemistry.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./stereochemistry.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./integrity_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./chain_mapping.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./chain_mapping.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/./testutils.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./mmseqs2.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./invalid_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./ligand_scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./ligand_scoring.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build +[ 0%] Built target scene_icons +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./stereochemistry.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./stereochemistry.py -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh +make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh -[ 0%] Built target scene_icons +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh +[ 0%] Built target ost_seq_alg_pymod +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dockq.py make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./dockq.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/bindings/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dockq.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./ptr_observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./ligand_scoring.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./ligand_scoring.py -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log.hh -make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build -[ 0%] Built target ost_bindings_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/stereo_data.json /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_data.json +make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_list.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/./dockq.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./dockq.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./conop.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py +[ 0%] Built target ost_bindings_headers make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh [ 0%] Built target ost_base_pymod -[ 0%] Built target ost_bindings_pymod -make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./log_sink.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./processor.hh +[ 0%] Built target ost_bindings_pymod make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" -make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/pymod/stereo_data.json /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/stereo_data.json -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_item.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py +make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend +make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec2.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./module_config.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build -make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh +[ 0%] Built target ost_mol_alg_pymod +make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./anisotropic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh -[ 0%] Built target ost_mol_alg_pymod -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh -make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_path.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./dyn_cast.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./diag.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec3.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec4.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_set.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./model_check.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./sequence_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clear.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clear.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./stdint_msc.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./heuristic.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/star_parser.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./linear_indexer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_region.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./range.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./binary_container.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./range.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/render_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh -[ 0%] Built target ost_db_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./units.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./convolute.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./message.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./module_config.hh +[ 0%] Built target ost_db_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/io_profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/scene_selection_helper.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/./item_type_cast.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./message.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./rule_based.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/simple_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./platform.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target ost_seq_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh -make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/./profile_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh -[ 0%] Built target ost_info_headers -make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend -[ 0%] Built target ost_conop_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./string_ref.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/sline_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh +[ 0%] Built target ost_info_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh +make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./dft.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/./ring_finder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./local_dist_diff_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./pod_vector.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 0%] Built target ost_seq_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh +make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh +[ 0%] Built target ost_conop_headers +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./forcefield.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fft.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./fixed_string.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite2_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./ff_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./tri_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./buildingblock.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fill.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./forcefield.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/./paged_array.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./ff_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh [ 0%] Built target ost_base_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/index.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./buildingblock.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./interaction.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./quat.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./settings.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh +[ 0%] Built target ost_config +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./transform.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 0%] Built target ost_config -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./simulation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./point_cloud.hh +[ 0%] Built target ost_gui_scene_pymod cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_base.hh -[ 0%] Built target ost_gui_scene_pymod -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./modeller.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./circle_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/save_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./interaction.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./histogram.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./settings.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./settings.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh [ 0%] Built target ost_geom_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./composite_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./simulation.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/tool_options_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_entity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./atom_view.hh +[ 0%] Built target ost_seq_alg_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./state_extractor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/mouse_event.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_algorithm.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./modeller.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/mat2.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -MF CMakeFiles/ost_geom.dir/mat4.cc.o.d -o CMakeFiles/ost_geom.dir/mat4.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/mat4.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/mat2.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -MF CMakeFiles/ost_geom.dir/mat3.cc.o.d -o CMakeFiles/ost_geom.dir/mat3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/mat3.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./system_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bond_table.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/load_surface.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data_types.hh -[ 0%] Built target ost_seq_alg_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./data.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -MF CMakeFiles/ost_geom.dir/vec3.cc.o.d -o CMakeFiles/ost_geom.dir/vec3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/vec3.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./debug.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./steep.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_view.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./state_extractor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./dllexport.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./dllexport.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./system_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chain_type.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/sdf_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_iterator.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_log.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh -[ 0%] Built target ost_mol_mm_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_class.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology_creator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/mmcif_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./norm_od.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh -[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./index.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./index.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./extent.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/vecmat2_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./chem_type.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./molck.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/mol/omf.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./topology.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh +[ 0%] Built target ost_mol_alg_headers cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_factory.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_factory.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/load_map.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/mm/src/./steep.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mm/./steep.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh +[ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./randomize.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/vecmat2_op.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/image_format.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh -[ 0%] Built target ost_mol_alg_headers +[ 0%] Built target ost_mol_mm_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./coord_frame.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat3_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/vecmat3_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./threshold.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./mol.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./image.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/tick_painter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./inverted_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/title_row.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_mirror.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./map.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_view.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_visitor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/tiff_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/img/jpk_util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./transformations.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./ics_editor.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./polar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./normalizer_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./property_id.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./line_average.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./line_average.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/./rscrosscorr.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_pass.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_error.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./observable.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh [ 0%] Built target ost_img_alg_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./paste_impl.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/vecmat4_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./peak.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/load.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/load.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./color.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./phase.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/seq/save.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/seq/save.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./residue_view.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./physical_units.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./sec_structure.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./sec_structure.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_manager.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./binary_data_source.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./point.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_builder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./builder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./container_serialization.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_handle.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./swap_util.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./surface_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./surface_prop.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./size.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_utils.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_exception.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./torsion_handle.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./transfer_connectivity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./convert.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./query_view_wrapper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./converting_streams.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./formatted_line.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh -[ 1%] Built target ost_img_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/state.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./vecmat.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh +[ 1%] Built target ost_img_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -MF CMakeFiles/ost_geom.dir/composite2.cc.o.d -o CMakeFiles/ost_geom.dir/composite2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./star_parser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./input.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./input.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/bottom_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./prim_list.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./prim_list.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/button_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/button_box.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_info.hh +[ 1%] Built target ost_mol_headers +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/event_button.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./io_profile.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./bounding_box.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./dcd_io.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite3.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_widget_container.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./selection.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./surface.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/panel_bar_widget_holder.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./texture.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/side_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/splitter_panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh -[ 1%] Built target ost_mol_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/panels/tabbed_panel_bar.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite3.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/context_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gl_include.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/current_selection_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./glext_include.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/custom_part_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_writer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/entity_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/entity_part_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/gfx_scene_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_writer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/label_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/root_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_entity.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/render_mode_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./povray.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_surface.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/sdf_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sdf_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/mmcif_str.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./mmcif_str.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./omf.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_slab.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh [ 1%] Built target ost_gfx_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/load.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./save.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/load_map.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./image_format.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/tiff_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./tiff_util.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/io/./jpk_util.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh [ 1%] Built target ost_io_headers -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite3_op.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -MF CMakeFiles/ost_geom.dir/quat.cc.o.d -o CMakeFiles/ost_geom.dir/quat.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/quat.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_browser.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_viewer.hh In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.cc:23: /build/reproducible-path/openstructure-2.5.0/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -3780,19 +3801,34 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/transform.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gl_win.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_menu.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./gosty_app.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./admin.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./module_config.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main.hh +[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/aligned_cuboid.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_area.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./perspective.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./scene_selection.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./main_window.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./dock_widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget.hh +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget_pool.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget_registry.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./widget_state_saver.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gui/src/./file_loader.hh /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 1%] Built target ost_gui_headers -[ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/aligned_cuboid.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/src/point_cloud.cc +[ 1%] Built target ost_gui_headers In file included from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2_op.cc:24: @@ -3819,9 +3855,9 @@ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 1%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend -make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake "--color=" +make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' @@ -3830,36 +3866,36 @@ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o [ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/log_sink.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -MF CMakeFiles/ost_base.dir/generic_property.cc.o.d -o CMakeFiles/ost_base.dir/generic_property.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/generic_property.cc -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -[ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o +[ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o +[ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o +[ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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modules/base/src/CMakeFiles/ost_base.dir/units.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c 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-I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/message.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/test_utils/compare_files.cc +[ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/boost_filesystem_helper.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o @@ -3889,7 +3925,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -3903,7 +3939,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3916,7 +3952,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -3930,7 +3966,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3943,7 +3979,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -3957,7 +3993,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3970,34 +4006,14 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4011,23 +4027,10 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, @@ -4038,13 +4041,19 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4076,7 +4085,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4090,7 +4099,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4100,6 +4109,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4130,7 +4141,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4144,7 +4155,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat4_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4157,7 +4168,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4171,7 +4182,34 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4181,12 +4219,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4214,14 +4246,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc -[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_transform.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3_op.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.cc +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4251,7 +4285,7 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4265,7 +4299,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4275,27 +4309,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite3.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_transform.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4320,18 +4335,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_item.cc +[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_path.cc +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4345,7 +4358,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4382,12 +4395,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_path.cc -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_visitor.cc +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/geom_info_conversion.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4414,10 +4425,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/geom_info_conversion.cc -[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4447,6 +4454,35 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_quat.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/geom_info_conversion.cc:19: @@ -4493,62 +4529,66 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 6%] Linking CXX shared library ../../../stage/lib/libost_info.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_info.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.5 -o ../../../stage/lib/libost_info.so.2.5.0 CMakeFiles/ost_info.dir/info_impl.cc.o CMakeFiles/ost_info.dir/info_handle.cc.o CMakeFiles/ost_info.dir/info_group.cc.o CMakeFiles/ost_info.dir/info_item.cc.o CMakeFiles/ost_info.dir/info_path.cc.o CMakeFiles/ost_info.dir/info_set.cc.o CMakeFiles/ost_info.dir/info_visitor.cc.o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 [ 6%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 6%] Built target _ost_geom +make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && 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/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_logger.cc +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_range.cc +[ 6%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_units.cc +[ 6%] Linking CXX shared library ../../../stage/lib/libost_info.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_info.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.5 -o ../../../stage/lib/libost_info.so.2.5.0 CMakeFiles/ost_info.dir/info_impl.cc.o CMakeFiles/ost_info.dir/info_handle.cc.o CMakeFiles/ost_info.dir/info_group.cc.o CMakeFiles/ost_info.dir/info_item.cc.o CMakeFiles/ost_info.dir/info_path.cc.o CMakeFiles/ost_info.dir/info_set.cc.o 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../../../stage/lib/libost_info.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 6%] Built target ost_info make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -[ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o +[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o +[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o +[ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o +[ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF 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-ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.cc -[ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_base.cc -[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_algorithm.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -MF CMakeFiles/ost_img.dir/composite_mask.cc.o.d -o CMakeFiles/ost_img.dir/composite_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_algorithm.cc +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o +[ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF CMakeFiles/ost_img.dir/data.cc.o.d -o CMakeFiles/ost_img.dir/data.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 8%] Built target _ost_geom -make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 8%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/wrap_base.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -MF CMakeFiles/ost_img.dir/extent_iterator.cc.o.d -o CMakeFiles/ost_img.dir/extent_iterator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_iterator.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4571,26 +4611,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:28: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:26: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4627,37 +4663,23 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.hh:38, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:22: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data_observer.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4691,11 +4713,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -4704,34 +4730,8 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:20: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/list:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4741,8 +4741,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4751,6 +4749,7 @@ /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, @@ -4763,26 +4762,23 @@ /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.cc /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_view.cc:24: + from /usr/include/c++/13/list:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -4792,14 +4788,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4822,18 +4814,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_handle.cc -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_type.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.cc -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4862,6 +4844,32 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_base.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.hh:34, @@ -4886,10 +4894,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_type.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4915,8 +4929,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -4945,28 +4957,6 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, @@ -4994,24 +4984,17 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:27: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:24: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5021,25 +5004,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc +[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:24: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5049,24 +5031,33 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc -[ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_handle.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/inverted_mask.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5076,11 +5067,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5088,8 +5084,8 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5099,23 +5095,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5124,7 +5112,7 @@ from /usr/include/c++/13/stdexcept:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5139,20 +5127,16 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/map.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:32: + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5164,23 +5148,25 @@ | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/observable.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.cc -[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/scoped_ptr.hpp:23, + from /usr/include/boost/scoped_ptr.hpp:13, + from /usr/include/boost/smart_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base_fw.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5190,23 +5176,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:28: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5216,27 +5202,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_observer.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/composite_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/scoped_ptr.hpp:23, - from /usr/include/boost/scoped_ptr.hpp:13, - from /usr/include/boost/smart_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_base_fw.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_op.cc:21: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5246,11 +5229,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/phase.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -5259,8 +5246,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5270,17 +5256,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/phase.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.cc:26: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask.hh:28: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5304,10 +5303,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/physical_units.cc -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5335,24 +5330,35 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/physical_units.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/editor_base.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_observer.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:25: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_base.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5362,12 +5368,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5393,36 +5402,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_visitor.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc -[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/progress.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:30: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:28: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5432,19 +5429,42 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.cc +[ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_visitor.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.cc +[ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/progress.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5454,6 +5474,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5477,21 +5499,25 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/pixel_sampling.hh:30: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_property_mapper.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5501,20 +5527,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:25: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5524,28 +5554,19 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_mask.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/not_connected_error.cc -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.cc -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point_list.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:25: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5585,34 +5606,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/index.cc -[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/property_id.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:32: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/size.cc:27: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5622,8 +5627,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc +[ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5648,10 +5653,8 @@ | ^~~~~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_error.cc -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/not_connected_error.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5674,6 +5677,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/property_id.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5700,10 +5707,39 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.hh:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_error.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/ics_editor.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5733,10 +5769,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5759,6 +5791,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_state.cc +[ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5780,6 +5816,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5834,23 +5880,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5860,32 +5907,21 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:26: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_builder.cc:19: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5895,21 +5931,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.cc -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_view_wrapper.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/algorithm:60, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:19: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5919,22 +5952,33 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_handle.cc:26: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_view_wrapper.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc [ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/surface_handle.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: + from /usr/include/c++/13/algorithm:60, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -5944,8 +5988,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -5972,6 +6014,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6002,6 +6048,33 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc:1: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, @@ -6028,22 +6101,11 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 13%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6053,8 +6115,8 @@ from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6064,19 +6126,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6086,8 +6143,8 @@ from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/coord_source.cc:23: + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6097,24 +6154,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/view_op.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/in_mem_coord_source.cc:1: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:25: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6124,22 +6187,43 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc +[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:26: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 15%] Linking CXX shared library ../../../../stage/lib/libost_img.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.5 -o ../../../../stage/lib/libost_img.so.2.5.0 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5 ../../../../stage/lib/libost_img.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.hh:25: + from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, + from /usr/include/eigen3/Eigen/Core:19, + from /usr/include/eigen3/Eigen/Eigenvalues:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6149,11 +6233,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o +[ 15%] Built target ost_img +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 15%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc +[ 15%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc +[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, @@ -6180,26 +6275,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/xcs_editor.cc:26: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6209,51 +6296,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 15%] Linking CXX shared library ../../../../stage/lib/libost_img.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.5 -o ../../../../stage/lib/libost_img.so.2.5.0 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_img.so.2.5 ../../../../stage/lib/libost_img.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 15%] Built target ost_img -make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:26: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, - from /usr/include/eigen3/Eigen/Core:19, - from /usr/include/eigen3/Eigen/Eigenvalues:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/bounding_box.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6263,23 +6317,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 15%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:19: +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, + from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:17, + from /usr/include/boost/enable_shared_from_this.hpp:16, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6289,8 +6343,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_impl.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/connector_impl.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -6299,23 +6359,32 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/chain_impl.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, - from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:17, - from /usr/include/boost/enable_shared_from_this.hpp:16, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6325,6 +6394,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6348,16 +6425,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/dihedral.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_ast.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6378,35 +6447,24 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.cc -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:40: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 27 | class pointer_it : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6416,27 +6474,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.cc -[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh:22: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6446,10 +6500,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:40: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.cc +[ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc +[ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.cc +[ 17%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc +[ 17%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/atom_prop.cc +[ 17%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6485,6 +6558,47 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/settings.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/stutil.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table_selector.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/xmlrunner.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/testutils.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/query_impl.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 17%] Built target _ost_base +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 17%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6493,6 +6607,7 @@ /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, @@ -6513,6 +6628,33 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, @@ -6535,6 +6677,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -6543,16 +6687,17 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/convolute.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6560,7 +6705,8 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6570,6 +6716,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6578,16 +6730,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/auto_correlate.cc:21: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6604,8 +6756,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/cross_correlate.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -6624,6 +6776,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.cc +[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6631,36 +6789,10 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/correlate.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:36: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6669,16 +6801,19 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/density_slice.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6688,24 +6823,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/dft.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/module_config.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:31: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6715,6 +6836,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6740,25 +6865,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:36: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.cc:22: + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6768,29 +6895,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.cc -[ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fourier_filters.cc:25: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6800,16 +6920,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer_factory.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6835,28 +6949,26 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_logger.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc:4: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc:1: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6891,22 +7003,28 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_iterator.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:30: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6916,23 +7034,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/histogram.cc:25: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -6942,8 +7064,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer_factory.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc +[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -6982,15 +7106,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/mask_image.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7027,18 +7152,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 18%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_range.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc -[ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/smooth_mask_image.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o @@ -7081,8 +7194,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7103,6 +7216,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7112,8 +7229,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_log.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_linear.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7165,8 +7282,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7175,16 +7292,16 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/power_spectrum.cc:21: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7194,6 +7311,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc +[ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.5 -o ../../../../stage/lib/libost_mol.so.2.5.0 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7202,8 +7326,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/randomize.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7221,25 +7345,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/smooth_mask_image.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7249,27 +7370,25 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Linking CXX shared library ../../../../stage/lib/libost_mol.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.5 -o ../../../../stage/lib/libost_mol.so.2.5.0 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:32: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/smooth_mask_image.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7279,39 +7398,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_mol.so.2.5 ../../../../stage/lib/libost_mol.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 20%] Built target ost_mol make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:32: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7321,8 +7431,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 20%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.cc +[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7350,21 +7467,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:32: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:30: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.cc:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7378,20 +7496,18 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_shift.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7401,24 +7517,21 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7428,8 +7541,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 20%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/pymod/export_units.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7438,8 +7551,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_transform.cc:21: + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/threshold.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7457,24 +7570,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc +[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/discrete_shrink.cc:21: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7508,6 +7626,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7530,35 +7650,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc -[ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_handle.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.cc [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_column.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/fractional_shift.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7572,11 +7686,11 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -7584,7 +7698,7 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/polar.hh:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7619,41 +7733,11 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc [ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/rscrosscorr.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_list_impl.cc:23: @@ -7675,6 +7759,9 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.cc +[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7701,27 +7788,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.cc -[ 21%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/profile_handle.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_column.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7731,14 +7813,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -7782,31 +7856,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 21%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img_alg.so.2.5 -o ../../../../stage/lib/libost_img_alg.so.2.5.0 CMakeFiles/ost_img_alg.dir/anisotropic.cc.o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o CMakeFiles/ost_img_alg.dir/convolute.cc.o CMakeFiles/ost_img_alg.dir/correlate.cc.o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o CMakeFiles/ost_img_alg.dir/density_slice.cc.o CMakeFiles/ost_img_alg.dir/dft.cc.o CMakeFiles/ost_img_alg.dir/fft.cc.o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o CMakeFiles/ost_img_alg.dir/gaussian.cc.o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o CMakeFiles/ost_img_alg.dir/histogram.cc.o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o CMakeFiles/ost_img_alg.dir/mask_image.cc.o CMakeFiles/ost_img_alg.dir/normalizer.cc.o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o CMakeFiles/ost_img_alg.dir/norm_log.cc.o CMakeFiles/ost_img_alg.dir/norm_od.cc.o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o CMakeFiles/ost_img_alg.dir/randomize.cc.o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o CMakeFiles/ost_img_alg.dir/stat.cc.o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o CMakeFiles/ost_img_alg.dir/threshold.cc.o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o CMakeFiles/ost_img_alg.dir/transformations.cc.o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o CMakeFiles/ost_img_alg.dir/polar.cc.o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o CMakeFiles/ost_img_alg.dir/line_average.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.5.0 ../../../../stage/lib/libost_img_alg.so.2.5 ../../../../stage/lib/libost_img_alg.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 21%] Built target ost_img_alg +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:31: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc:23: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc:19: + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7816,27 +7889,20 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:24: +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:32: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/invalid_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:24: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7866,19 +7933,44 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/alignment_handle.cc:32: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_op.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -7918,78 +8010,51 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/sequence_list.cc:31: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 21%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/settings.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/stutil.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/table_selector.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/xmlrunner.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/base/pymod/testutils.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" [ 22%] Linking CXX shared library ../../../../stage/lib/libost_seq.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq.so.2.5 -o ../../../../stage/lib/libost_seq.so.2.5.0 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 22%] Built target _ost_base -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 22%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/pymod/wrap_info.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.5.0 ../../../../stage/lib/libost_seq.so.2.5 ../../../../stage/lib/libost_seq.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 22%] Built target ost_seq make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend -make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake "--color=" +make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/db/src 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modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o +[ 22%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc +[ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -[ 24%] Building CXX object 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/usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/sqlite_wrap.cc [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG 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/build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -[ 24%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/sqlite_wrap.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o 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/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o 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/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/linear_indexer.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_weight_matrix.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o 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-g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_weight_matrix.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc In file included from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:7, from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:20: @@ -8019,10 +8084,14 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:705:14: warning: statement has no effect [-Wunused-value] 705 | for (j;j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 878 | for (i=0;i >&, const std::vector >&, std::string, std::string)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1604:38: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] 1604 | if (atom_site_pos==_atom_site["Cartn_x"]) @@ -8085,6 +8154,32 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/se.h:44:9: warning: unused variable 'i' [-Wunused-variable] 44 | int i,j; | ^ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'double homo_refined_greedy_search(double**, int*, int*, int, int, double**, double**, double, int, double**)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:440:12: warning: unused variable 'TMnow' [-Wunused-variable] 440 | double TMnow =0; @@ -8110,12 +8205,20 @@ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:1166:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1166 | for (i=0;i struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void copy_chain_assign_data(int, int, std::vector >&, std::vector > >&, std::vector > >&, int*, int*, double**, std::vector > >&, std::vector > >&, int*, int*, double**)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:1590:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1590 | for (i=0;i >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2528:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] 2528 | double Lnorm_d0; @@ -8140,15 +8243,14 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8158,16 +8260,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/ins_del.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8176,14 +8268,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8227,28 +8320,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.hh:22: +In file included from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8260,18 +8343,15 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh: At global scope: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/param_set.h:6, - from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:6: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8289,15 +8369,9 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/entropy.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ @@ -8309,18 +8383,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8330,6 +8403,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8338,15 +8419,18 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/contact_prediction_score.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh: At global scope: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/param_set.h:6, + from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:6: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8357,15 +8441,6 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ @@ -8373,16 +8448,10 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/distance_map.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.cc +[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.cc In file included from /usr/include/c++/13/string:54, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -8458,14 +8527,15 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.cc -[ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/pair_subst_weight_matrix.cc [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/semiglobal_align.cc +[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_identity.cc +[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_similarity.cc +[ 25%] Linking CXX shared library ../../../stage/lib/libost_db.so In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -8474,19 +8544,17 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/impl/align_impl.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/global_align.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/ins_del.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/global_align.cc:19: +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_db.dir/link.txt --verbose=1 +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8496,8 +8564,7 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/sequence_identity.cc +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.5 -o ../../../stage/lib/libost_db.so.2.5.0 CMakeFiles/ost_db.dir/sqlite_wrap.cc.o CMakeFiles/ost_db.dir/linear_indexer.cc.o CMakeFiles/ost_db.dir/binary_container.cc.o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -8506,20 +8573,12 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Linking CXX shared library ../../../stage/lib/libost_db.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_db.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.5 -o ../../../stage/lib/libost_db.so.2.5.0 CMakeFiles/ost_db.dir/sqlite_wrap.cc.o CMakeFiles/ost_db.dir/linear_indexer.cc.o CMakeFiles/ost_db.dir/binary_container.cc.o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.5.0 ../../../stage/lib/libost_db.so.2.5 ../../../stage/lib/libost_db.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 25%] Built target ost_db -make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/processor.cc +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8555,18 +8617,19 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:4: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -8998,19 +9042,19 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:5, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/minimal_compound_lib.hh:5, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/minimal_compound_lib.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc:20: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9020,8 +9064,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -MF CMakeFiles/ost_conop.dir/rule_based.cc.o.d -o CMakeFiles/ost_conop.dir/rule_based.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/rule_based.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9073,14 +9115,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.cc -[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound.cc -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.cc -[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -MF CMakeFiles/ost_conop.dir/ring_finder.cc.o.d -o CMakeFiles/ost_conop.dir/ring_finder.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9106,6 +9140,36 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.cc +make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend +[ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound.cc +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc +[ 26%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/ring_finder.cc.o -MF CMakeFiles/ost_conop.dir/ring_finder.cc.o.d -o CMakeFiles/ost_conop.dir/ring_finder.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc +make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9194,6 +9258,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc In file included from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, @@ -9265,9 +9331,6 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.5 -o ../../../../stage/lib/libost_seq_alg.so.2.5.0 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, @@ -9394,233 +9457,39 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +[ 26%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.5 -o ../../../../stage/lib/libost_seq_alg.so.2.5.0 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../../../stage/lib/libost_mol.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.5.0 ../../../../stage/lib/libost_seq_alg.so.2.5 ../../../../stage/lib/libost_seq_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 26%] Built target ost_seq_alg -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2941:43: warning: 'dinter' may be used uninitialized [-Wmaybe-uninitialized] - 2941 | dinter_vec.push_back(make_pair(dinter,r1)); - | ~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2894:12: note: 'dinter' was declared here - 2894 | double dinter; - | ^~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, int)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:545:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] - 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 546 | mol_type, invmap, 0, glocal); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:535:14: note: 'invmap' was declared here - 535 | int *invmap; - | ^~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc: In function 'ost::bindings::MMAlignResult ost::bindings::WrappedMMAlign(const std::vector&, const std::vector&, const ost::seq::SequenceList&, const ost::seq::SequenceList&, const std::vector&, const std::vector&, bool)': -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'seqy' may be used uninitialized [-Wmaybe-uninitialized] - 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 900 | sequence, d0_scale, fast_opt); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:548:18: note: 'seqy' was declared here - 548 | char *seqx, *seqy; // for the protein sequence - | ^~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'secx' may be used uninitialized [-Wmaybe-uninitialized] - 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 900 | sequence, d0_scale, fast_opt); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:549:11: note: 'secx' was declared here - 549 | char *secx, *secy; // for the secondary structure - | ^~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'secy' may be used uninitialized [-Wmaybe-uninitialized] - 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 900 | sequence, d0_scale, fast_opt); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:549:18: note: 'secy' was declared here - 549 | char *secx, *secy; // for the secondary structure - | ^~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'seqx' may be used uninitialized [-Wmaybe-uninitialized] - 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 900 | sequence, d0_scale, fast_opt); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:548:11: note: 'seqx' was declared here - 548 | char *seqx, *seqy; // for the protein sequence - | ^~~~ -[ 26%] Linking CXX shared library ../../../stage/lib/libost_conop.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.5 -o ../../../stage/lib/libost_conop.so.2.5.0 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5 ../../../stage/lib/libost_conop.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 26%] Built target ost_conop -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/bitmap_io.cc -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -[ 26%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS 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/usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 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/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc -[ 26%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.cc:23: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:23: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.cc -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:20: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/config/no_tr1/memory.hpp:21, - from /usr/include/boost/get_pointer.hpp:14, - from /usr/include/boost/bind/mem_fn.hpp:25, - from /usr/include/boost/bind/bind.hpp:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9637,173 +9506,21 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:24: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/input.cc -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc:29: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc:20: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:32: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] - 55 | virtual void DeepSwap(GfxNode& n); - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' - 58 | virtual void DeepSwap(GfxObj& go); - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:36: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:23: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:28: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:24: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc -[ 27%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.cc -[ 29%] Linking CXX shared library ../../../stage/lib/libost_bindings.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:39: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:52: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' - 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.5 -o ../../../stage/lib/libost_bindings.so.2.5.0 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.hh:26: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.5.0 ../../../stage/lib/libost_bindings.so.2.5 ../../../stage/lib/libost_bindings.so -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 29%] Built target ost_bindings -[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:31: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/locale:41, - from /usr/include/boost/filesystem/detail/path_traits.hpp:18, - from /usr/include/boost/filesystem/path.hpp:21, - from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:25: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9813,28 +9530,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/info/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 30%] Built target _ost_info -make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] - 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' - 40 | virtual geom::AlignedCuboid GetBoundingBox() const; - | ^~~~~~~~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9842,63 +9537,21 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:26: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:40: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:23: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9911,19 +9564,25 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc:23: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -9933,8 +9592,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -9942,150 +9599,21 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:26: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:23: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:28: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] - 55 | virtual void DeepSwap(GfxNode& n); - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' - 58 | virtual void DeepSwap(GfxObj& go); - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:49: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] - 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; - | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:50: -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' - 40 | virtual geom::AlignedCuboid GetBoundingBox() const; - | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/locale:41, - from /usr/include/boost/filesystem/detail/path_traits.hpp:18, - from /usr/include/boost/filesystem/path.hpp:21, - from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:22: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.cc:20: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/iterator:61, - from /usr/include/boost/operators.hpp:98, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:28: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:24: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /usr/include/boost/format.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:23: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10095,26 +9623,13 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/texture.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc -[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] - 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] - 1239 | void render_aalines(AALineList& line_list, float w, float r) - | ^~~~~~~~~~~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'int trimComplex(std::vector > >&, std::vector >&, std::vector >&, std::vector&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, int, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2941:43: warning: 'dinter' may be used uninitialized [-Wmaybe-uninitialized] + 2941 | dinter_vec.push_back(make_pair(dinter,r1)); + | ~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2894:12: note: 'dinter' was declared here + 2894 | double dinter; + | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -10122,7 +9637,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10136,33 +9651,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10175,18 +9664,25 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10199,21 +9695,25 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_extent_iterator.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:22: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10223,13 +9723,17 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_handle.cc +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10237,7 +9741,13 @@ from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:19: + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10247,17 +9757,32 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc +[ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_phase.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_handle.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10267,26 +9792,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' - 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc:21: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10296,27 +9822,46 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc +[ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_point.cc +[ 27%] Linking CXX shared library ../../../stage/lib/libost_conop.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.5 -o ../../../stage/lib/libost_conop.so.2.5.0 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.5.0 /usr/lib/x86_64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.5.0 ../../../stage/lib/libost_conop.so.2.5 ../../../stage/lib/libost_conop.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 27%] Built target ost_conop +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_progress.cc +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'int extract_aln_from_resi(std::vector >&, char*, char*, std::vector >, std::vector >, int)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:545:21: warning: 'invmap' may be used uninitialized [-Wmaybe-uninitialized] + 545 | NWalign_main(seqx, seqy, xlen, ylen, sequence[0],sequence[1], + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 546 | mol_type, invmap, 0, glocal); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:535:14: note: 'invmap' was declared here + 535 | int *invmap; + | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:20: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10326,37 +9871,85 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' - 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc: In function 'ost::bindings::MMAlignResult ost::bindings::WrappedMMAlign(const std::vector&, const std::vector&, const ost::seq::SequenceList&, const ost::seq::SequenceList&, const std::vector&, const std::vector&, bool)': +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'seqy' may be used uninitialized [-Wmaybe-uninitialized] + 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 900 | sequence, d0_scale, fast_opt); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:548:18: note: 'seqy' was declared here + 548 | char *seqx, *seqy; // for the protein sequence + | ^~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'secx' may be used uninitialized [-Wmaybe-uninitialized] + 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 900 | sequence, d0_scale, fast_opt); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:549:11: note: 'secx' was declared here + 549 | char *secx, *secy; // for the secondary structure + | ^~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'secy' may be used uninitialized [-Wmaybe-uninitialized] + 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 900 | sequence, d0_scale, fast_opt); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:549:18: note: 'secy' was declared here + 549 | char *secx, *secy; // for the secondary structure + | ^~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:896:36: warning: 'seqx' may be used uninitialized [-Wmaybe-uninitialized] + 896 | if (byresi_opt==0) MMalign_iter(max_total_score, max_iter, xa_vec, ya_vec, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 897 | seqx_vec, seqy_vec, secx_vec, secy_vec, mol_vec1, mol_vec2, xlen_vec, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 898 | ylen_vec, xa, ya, seqx, seqy, secx, secy, len_aa, len_na, chain1_num, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 899 | chain2_num, TMave_mat, seqxA_mat, seqyA_mat, assign1_list, assign2_list, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 900 | sequence, d0_scale, fast_opt); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/bindings/src/wrap_tmalign.cc:548:11: note: 'seqx' was declared here + 548 | char *seqx, *seqy; // for the protein sequence + | ^~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10366,65 +9959,35 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc -[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:102:8: note: by 'ost::gfx::Surface::Apply' - 102 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point_list.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_point.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:23: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_point.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10434,22 +9997,52 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc +[ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 27%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc +[ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc +[ 29%] Linking CXX shared library ../../../stage/lib/libost_bindings.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.5 -o ../../../stage/lib/libost_bindings.so.2.5.0 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.5.0 ../../../stage/lib/libost_mol.so.2.5.0 ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.5.0 ../../../stage/lib/libost_bindings.so.2.5 ../../../stage/lib/libost_bindings.so +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 29%] Built target ost_bindings +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 29%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/bitmap_io.cc +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10459,22 +10052,28 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:20: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_size.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10484,55 +10083,27 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/mask.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:19: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:22: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_mask.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10542,26 +10113,28 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10571,27 +10144,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:27: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10601,76 +10176,36 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' - 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:25: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:24: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 27 | class pointer_it : public std::iterator{ + | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] - 55 | virtual void DeepSwap(GfxNode& n); - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' - 58 | virtual void DeepSwap(GfxObj& go); - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:26: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] - 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); - | ^~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' - 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); - | ^~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_list.cc:25: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10685,9 +10220,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10696,31 +10230,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/connect_renderer_base.cc:23: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10730,34 +10240,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:35, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc:22: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] - 55 | virtual void DeepSwap(GfxNode& n); - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' - 58 | virtual void DeepSwap(GfxObj& go); - | ^~~~~~~~ -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/tabulated_trig.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.cc -[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc -[ 32%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.cc +[ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer_base.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/exporter.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10774,75 +10264,31 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.cc +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/mapped_property.cc:20: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/custom_render_options.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/trace_renderer.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cpk_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/simple_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/sline_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/line_trace_render_options.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/fast_spheres.cc:28: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.cc:29: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:26: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10852,21 +10298,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.cc +[ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/input.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/render_options.cc:22: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10876,19 +10330,14 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/cartoon_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/render_options/trace_render_options.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/clash_score.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10897,47 +10346,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.cc -[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.cc -[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.cc -[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc -[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/map_handle_color_op.cc:20: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10950,7 +10359,11 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc:28: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -10958,10 +10371,8 @@ from /usr/include/c++/13/string:47, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen.cc:23: + from /usr/include/c++/13/iomanip:42, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10976,16 +10387,23 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/map.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_slab.cc:22: + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_map.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -10995,21 +10413,35 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:6: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 30%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:28: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_o.cc:21: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11022,23 +10454,17 @@ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_octree.cc:24: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:32: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gl_helper.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/primitives.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11048,24 +10474,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 30%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc:33: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_construct.h:61, - from /usr/include/c++/13/bits/stl_tempbuf.h:61, - from /usr/include/c++/13/memory:66, - from /usr/include/boost/smart_ptr/shared_array.hpp:21, - from /usr/include/boost/shared_array.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/map_iso_gen_s.cc:21: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_img.cc:27: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11075,25 +10507,30 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc +[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.cc +[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.cc +[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc +[ 31%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:36: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/map_iso.cc:23: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11108,9 +10545,9 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_structure_segments.cc:19: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11119,7 +10556,7 @@ from /usr/include/c++/13/cmath:3699, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11129,27 +10566,36 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:39: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] + 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); + | ^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.cc:52: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' + 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); + | ^~~~~ +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 31%] Built target _ost_img +[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_handle.hh:38, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/octree_isocont.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:21: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/iterator:61, - from /usr/include/boost/container_hash/is_range.hpp:16, - from /usr/include/boost/container_hash/hash.hpp:15, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_map.hpp:20, - from /usr/include/boost/unordered_map.hpp:17, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gl_helper.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11159,62 +10605,32 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o +[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/superpose_frames.cc -In file included from /usr/include/eigen3/Eigen/Core:341, - from /usr/include/eigen3/Eigen/QR:11, - from /usr/include/eigen3/Eigen/SVD:11, - from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc:26: -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] - 327 | internal::triangular_matrix_vector_product - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 328 | - | ~~~~~~~~~ - 332 | ::run(actualLhs.rows(),actualLhs.cols(), - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 333 | actualLhs.data(),actualLhs.outerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 334 | actualRhsPtr,1, - | ~~~~~~~~~~~~~~~ - 335 | dest.data(),dest.innerStride(), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 336 | actualAlpha); - | ~~~~~~~~~~~~ -/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here - 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc +[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_test_common.cc:1: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc:24: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11224,25 +10640,23 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:4: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/iomanip:42, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:1: +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/config/no_tr1/memory.hpp:21, + from /usr/include/boost/get_pointer.hpp:14, + from /usr/include/boost/bind/mem_fn.hpp:25, + from /usr/include/boost/bind/bind.hpp:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11252,18 +10666,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/local_dist_diff_test.cc:6: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11303,10 +10705,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc +[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11314,7 +10714,8 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc:20: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:27: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11325,7 +10726,7 @@ from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11340,9 +10741,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc:23: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11356,7 +10755,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain.cc:19: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11366,6 +10765,15 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.cc:32: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] + 55 | virtual void DeepSwap(GfxNode& n); + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' + 58 | virtual void DeepSwap(GfxObj& go); + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11400,38 +10808,7 @@ from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_atom_view.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc:24: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -11445,76 +10822,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bond.cc:19: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:4: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:1: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:27: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:23: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:21: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:20: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11524,22 +10832,29 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 31%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc +[ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc +[ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:24: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11549,12 +10864,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.cc -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc +[ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.cc In file included from /usr/include/c++/13/string:54: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:869:23, @@ -11748,6 +11059,372 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +[ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc +[ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/filter_clashes.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_residue_view.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc:26: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/wrap_alg.cc:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:4: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/construct_cbeta.cc:1: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/trajectory_analysis.cc:23: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:31: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/locale:41, + from /usr/include/boost/filesystem/detail/path_traits.hpp:18, + from /usr/include/boost/filesystem/path.hpp:21, + from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.cc:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] + 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' + 40 | virtual geom::AlignedCuboid GetBoundingBox() const; + | ^~~~~~~~~~~~~~ +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_surface.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc:30: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_filter.cc:27: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/input.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/structure_analysis.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_bounding_box.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/log.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/consistency_checks.cc:20: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/prim_list.cc:23: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11782,8 +11459,70 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image_state.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc:30: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_normalizer.cc:27: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:40: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:23: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:49: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:124:31: warning: 'virtual geom::AlignedCuboid ost::gfx::GfxObj::GetBoundingBox(bool) const' was hidden [-Woverloaded-virtual=] + 124 | virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const; + | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.cc:50: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_test_object.hh:40:31: note: by 'virtual geom::AlignedCuboid ost::gfx::GfxTestObj::GetBoundingBox() const' + 40 | virtual geom::AlignedCuboid GetBoundingBox() const; + | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11810,6 +11549,91 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.hh:9, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.cc +[ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc +[ 34%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_torsion.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc:28: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_transcendentals.cc:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/export_polar.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11847,41 +11671,50 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.hh:9, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.cc:24: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/selection.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc -[ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.hh:7, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc:1: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:26: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.hh:5: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/stl_tree.h:63, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11891,6 +11724,8 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, @@ -11919,25 +11754,46 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/surface.cc:28: +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] + 55 | virtual void DeepSwap(GfxNode& n); + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' + 58 | virtual void DeepSwap(GfxObj& go); + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:9: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:1: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11947,30 +11803,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc -[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/find_membrane.cc -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:9: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 32 | : public std::iterator{ - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:1: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.cc:19: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/vector:62, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient.hh:26: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -11980,51 +11824,25 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc -In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, - inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:117:30, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:33: -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] - 10 | struct ExtendedBridge { - | ^~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here - 87 | extended_bridges.push_back(ExtendedBridge()); - | ^ -In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', - inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, - inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, - inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:468:28, - inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:123:21, - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, - inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:33: -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] - 10 | struct ExtendedBridge { - | ^~~~~~~~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': -/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here - 87 | extended_bridges.push_back(ExtendedBridge()); - | ^ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:27: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/image.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.hh:7, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, - from /usr/include/c++/13/stdexcept:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:24: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12034,11 +11852,16 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Linking CXX shared library ../../../stage/lib/libost_gfx.so -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/test_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/test_texture.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/glyph_texture.png /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG 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../../../stage/lib/libost_info.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc +[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc +[ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc +[ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc +[ 35%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.cc In file included from /usr/include/c++/13/string:54: In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:869:23, @@ -12106,56 +11929,6 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/find_membrane.cc:1: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc:1: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 25 | class const_circular_iter : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 100 | class circular_iter : public std::iterator - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In member function 'bool std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_is_local() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:869:23, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, @@ -12345,19 +12118,211 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.5.0 ../../../stage/lib/libost_gfx.so.2.5 ../../../stage/lib/libost_gfx.so -[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc -make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 37%] Built target ost_gfx -make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake "--color=" +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:1: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:1: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 36%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/locale:41, + from /usr/include/boost/filesystem/detail/path_traits.hpp:18, + from /usr/include/boost/filesystem/path.hpp:21, + from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gradient_manager.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc +[ 37%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 /usr/lib/x86_64-linux-gnu/libfftw3f.so /usr/lib/x86_64-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.5.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 +In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, + inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:117:30, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:33: +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] + 10 | struct ExtendedBridge { + | ^~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here + 87 | extended_bridges.push_back(ExtendedBridge()); + | ^ +In constructor '{anonymous}::ExtendedBridge::ExtendedBridge({anonymous}::ExtendedBridge&&)', + inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/new_allocator.h:191:4, + inlined from 'static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = {anonymous}::ExtendedBridge; _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge]' at /usr/include/c++/13/bits/alloc_traits.h:538:17, + inlined from 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:468:28, + inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {{anonymous}::ExtendedBridge}; _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/vector.tcc:123:21, + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = {anonymous}::ExtendedBridge; _Alloc = std::allocator<{anonymous}::ExtendedBridge>]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, + inlined from 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:33: +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:10:8: warning: '.{anonymous}::ExtendedBridge::parallel' may be used uninitialized [-Wmaybe-uninitialized] + 10 | struct ExtendedBridge { + | ^~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc: In function 'bool {anonymous}::AddIfValid(int, int, int, int, const std::vector&, bool, std::vector&)': +/build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/sec_struct.cc:87:49: note: '' declared here + 87 | extended_bridges.push_back(ExtendedBridge()); + | ^ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/img/alg/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" +In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:11: +In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', + inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, + inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:363:37: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: '*(uint64_t*)' may be used uninitialized [-Wmaybe-uninitialized] + 109 | data_[byte_index] &= ~(one << bit_index); + | ~~~~~~~~~~~~~~~~^ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build -make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' -[ 37%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc +[ 37%] Built target _ost_img_alg +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_visitor.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/conop.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/message.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/nonstandard.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc:1: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.cc +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/find_membrane.cc In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/molck.cc:4: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/sstream:40, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc:1: +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12492,37 +12450,17 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc -In file included from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:11: -In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', - inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, - inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.cc:363:37: -/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: '*(uint64_t*)' may be used uninitialized [-Wmaybe-uninitialized] - 109 | data_[byte_index] &= ~(one << bit_index); - | ~~~~~~~~~~~~~~~~^ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc:22: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.cc:23: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_chain_view.cc:19: + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12532,30 +12470,18 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 37%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_phase.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.hh:34, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:25: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data_algorithm.cc:25: + from /usr/include/c++/13/vector:62, + from /usr/include/boost/format.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12565,27 +12491,22 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc +[ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc:28: + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/material.cc:20: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algobase.h:65, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_data.cc:25: +In file included from /usr/include/c++/13/iterator:61, + from /usr/include/boost/operators.hpp:98, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:28: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12595,14 +12516,17 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/extent.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/wrap_extent_iterator.hh:34, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:26: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -12616,7 +12540,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_extent.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12626,28 +12550,36 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/texture.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] + 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] + 1239 | void render_aalines(AALineList& line_list, float w, float r) + | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_handle.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/mol.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/find_membrane.cc:1: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_image_handle.cc:25: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -12657,10 +12589,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_point.cc -[ 39%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_group.cc In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, @@ -12996,13 +12924,612 @@ /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ +[ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/povray.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/point.hh:35, - from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/peak.hh:31, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc:29: + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/data.hh:36, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/algorithm.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc:10: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/entity_to_density.cc:1: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:27: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/sstream:40, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/gost_exporter.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/color_op.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_element_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] + 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); + | ^~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' + 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); + | ^~~~~ +[ 39%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.5.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../../../stage/lib/libost_info.so.2.5.0 ../../../../stage/lib/libost_base.so.2.5.0 ../../../../stage/lib/libost_geom.so.2.5.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.83.0 /usr/lib/x86_64-linux-gnu/libQt5Xml.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5.15.10 /usr/lib/x86_64-linux-gnu/libQt5Core.so.5.15.10 +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:19: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/uniform_color_op.cc:20: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_color_op.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:41, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/by_chain_color_op.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] + 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); + | ^~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' + 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); + | ^~~~~ +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 39%] Built target _ost_mol +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.5.0 /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build +make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' +[ 39%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/entity_view_color_op.cc:21: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/vector:62, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:25: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_handle.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:31: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/dyn_cast.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_profile_handle.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/color_ops/basic_gradient_color_op.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] + 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); + | ^~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/surface.hh:102:8: note: by 'ost::gfx::Surface::Apply' + 102 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); + | ^~~~~ +[ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/view_op.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_renderer.cc:23: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:22: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/entity_detail.cc:20: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cartoon_renderer.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec2.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/custom_renderer.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:24, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.hh:22: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 40%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/wrap_seq.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:62:16: warning: 'virtual void ost::gfx::GfxObj::Apply(ost::gfx::GfxNodeVisitor&, ost::gfx::GfxNodeVisitor::Stack)' was hidden [-Woverloaded-virtual=] + 62 | virtual void Apply(GfxNodeVisitor& v, GfxNodeVisitor::Stack st); + | ^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/cpk_renderer.cc:23: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity.hh:294:8: note: by 'ost::gfx::Entity::Apply' + 294 | void Apply(const gfx::MapHandleColorOp& op, bool store=true); + | ^~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/debug_renderer.cc:19: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:34, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:38: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:55:16: warning: 'virtual void ost::gfx::GfxNode::DeepSwap(ost::gfx::GfxNode&)' was hidden [-Woverloaded-virtual=] + 55 | virtual void DeepSwap(GfxNode& n); + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:58:16: note: by 'virtual void ost::gfx::GfxObj::DeepSwap(ost::gfx::GfxObj&)' + 58 | virtual void DeepSwap(GfxObj& go); + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_construct.h:61, + from /usr/include/c++/13/bits/stl_tempbuf.h:61, + from /usr/include/c++/13/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/sline_renderer.hh:27: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/color.hh:31, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/scene.hh:37, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:25: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47, + from /usr/include/c++/13/stdexcept:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/vec3.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/simple_renderer.cc:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query_state.hh:26, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:39, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/line_trace_renderer.cc:24: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 25 | class const_circular_iter : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:65, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/module_config.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:24: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 100 | class circular_iter : public std::iterator + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite2.hh:27, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/composite.hh:22, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/geom.hh:28, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info_group.hh:33, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/info/info.hh:32, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc:30: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ @@ -13016,7 +13543,7 @@ from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_peak.cc:25: + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -13026,14 +13553,40 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 39%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_coord_frame.cc -[ 39%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_progress.cc -[ 39%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/export_editors.cc -[ 39%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/pymod/export_raster_image.cc +[ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o +cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/gfx/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/x86_64-linux-gnu/qt5 -isystem /usr/include/x86_64-linux-gnu/qt5/QtXml -isystem /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem /usr/include/x86_64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/gfx/src/impl/backbone_trace.cc +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, + from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc:34: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 32 | : public std::iterator{ + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, + from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/pymod/export_sequence.cc:37: +/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 29 | class AlignedColumnIterator : public std::iterator