I: pbuilder: network access will be disabled during build 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 W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [openstructure_2.5.0-2.dsc] I: copying [./openstructure_2.5.0.orig.tar.xz] I: copying [./openstructure_2.5.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Apr 24 06:10:40 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./openstructure_2.5.0-2.dsc: no acceptable signature found dpkg-source: info: extracting openstructure in openstructure-2.5.0 dpkg-source: info: unpacking openstructure_2.5.0.orig.tar.xz dpkg-source: info: unpacking openstructure_2.5.0-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python-dist-packages.patch dpkg-source: info: applying fix-quotes-in-ENV.patch dpkg-source: info: applying skip-network-tests.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying ost_config.patch 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/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 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 ' 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=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 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 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 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 Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev, libopenmm-plugins, libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib, python3-numpy, python3-pil, python3-pyqt5, python3-scipy, qtbase5-dev, voronota dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19700 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dssp; however: Package dssp is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libglu1-mesa-dev; however: Package libglu1-mesa-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-plugins; however: Package libopenmm-plugins is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libqt5opengl5-dev; however: Package libqt5opengl5-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff-dev; however: Package libtiff-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on python3-pyqt5; however: Package python3-pyqt5 is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on qtbase5-dev; however: Package qtbase5-dev is not installed. pbuilder-satisfydepends-dummy depends on voronota; however: Package voronota is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} clustalw{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dssp{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono-dev{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-container-dev{a} libboost-container1.83-dev{a} libboost-container1.83.0{a} libboost-context-dev{a} libboost-context1.83-dev{a} libboost-context1.83.0{a} libboost-coroutine-dev{a} libboost-coroutine1.83-dev{a} libboost-coroutine1.83.0{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.83-dev{a} libboost-fiber-dev{a} libboost-fiber1.83-dev{a} libboost-fiber1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.83-dev{a} libboost-graph-parallel1.83.0{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-json-dev{a} libboost-json1.83-dev{a} libboost-json1.83.0{a} libboost-locale-dev{a} libboost-locale1.83-dev{a} libboost-locale1.83.0{a} libboost-log-dev{a} libboost-log1.83-dev{a} libboost-log1.83.0{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.83-dev{a} libboost-mpi-python1.83.0{a} libboost-mpi1.83-dev{a} libboost-mpi1.83.0{a} libboost-nowide-dev{a} libboost-nowide1.83-dev{a} libboost-nowide1.83.0{a} libboost-numpy-dev{a} libboost-numpy1.83-dev{a} libboost-numpy1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-random-dev{a} libboost-random1.83-dev{a} libboost-random1.83.0{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization-dev{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.83-dev{a} libboost-stacktrace1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.83-dev{a} libboost-type-erasure1.83.0{a} libboost-url-dev{a} libboost-url1.83-dev{a} libboost-url1.83.0{a} libboost-wave-dev{a} libboost-wave1.83-dev{a} libboost-wave1.83.0{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libbsd0{a} libcbor0.10{a} libcifpp-data{a} libcifpp5{a} libcom-err2{a} libcups2t64{a} libcurl4t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgfortran-13-dev{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm17t64{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopengl-dev{a} libopengl0{a} libopenjp2-7{a} libopenmm-dev{a} libopenmm-plugins{a} libopenmm8.1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpng-dev{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpthread-stubs0-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libqhull-r8.0{a} libqt5concurrent5t64{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5opengl5-dev{a} libqt5opengl5t64{a} libqt5printsupport5t64{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5widgets5t64{a} libqt5xml5t64{a} libraqm0{a} librdmacm1t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv-dev{a} libsharpyuv0{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtcl8.6{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtk8.6{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdecoder3{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-appdirs{a} python3-attr{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} qt5-qmake{a} qt5-qmake-bin{a} qtbase5-dev{a} qtbase5-dev-tools{a} qtchooser{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} voronota{a} x11-common{a} x11proto-dev{a} xkb-data{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libldap-common libmail-sendmail-perl libpng-tools libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-olefile qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xauth xdg-user-dirs 0 packages upgraded, 444 newly installed, 0 to remove and 0 not upgraded. Need to get 300 MB of archives. After unpacking 1537 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-1 [94.1 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-1.2 [28.2 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.7p1-4 [965 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 63 http://deb.debian.org/debian unstable/main amd64 clustalw amd64 2.1+lgpl-7 [282 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-3 [148 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1+b1 [10.7 MB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 87 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libcifpp-data all 5.0.7.1-3 [452 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libcifpp5 amd64 5.0.7.1-3+b1 [870 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 dssp amd64 4.2.2-2 [624 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14-20240429-1 [836 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get: 106 http://deb.debian.org/debian unstable/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 116 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-2.1+b1 [10.6 MB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-2.1+b1 [235 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-atomic-dev amd64 1.83.0.2+b2 [3904 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-2.1+b1 [239 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-2.1+b1 [244 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-chrono-dev amd64 1.83.0.2+b2 [4224 B] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83.0 amd64 1.83.0-2.1+b1 [259 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libboost-container1.83-dev amd64 1.83.0-2.1+b1 [264 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libboost-container-dev amd64 1.83.0.2+b2 [4072 B] Get: 137 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-2.1+b1 [230 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-2.1+b1 [332 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-2.1+b1 [372 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-2.1+b1 [239 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-2.1+b1 [230 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-2.1+b1 [231 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-2.1+b1 [269 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-2.1+b1 [277 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83.0 amd64 1.83.0-2.1+b1 [231 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-context1.83-dev amd64 1.83.0-2.1+b1 [232 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-context-dev amd64 1.83.0.2+b2 [3804 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libboost-coroutine-dev amd64 1.83.0.2+b2 [3868 B] Get: 151 http://deb.debian.org/debian unstable/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 152 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.83-dev amd64 1.83.0-2.1+b1 [230 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libboost-exception-dev amd64 1.83.0.2+b2 [3584 B] Get: 155 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-2.1+b1 [280 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-2.1+b1 [295 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83.0 amd64 1.83.0-2.1+b1 [253 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libboost-fiber1.83-dev amd64 1.83.0-2.1+b1 [264 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libboost-fiber-dev amd64 1.83.0.2+b2 [4028 B] Get: 160 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 161 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-2.1+b1 [358 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-2.1+b1 [325 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-2.1+b1 [342 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-2.1+b1 [466 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-2.1+b1 [537 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-2.1+b1 [383 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 169 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [132 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [54.1 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83.0 amd64 1.83.0-2.1+b1 [271 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83.0 amd64 1.83.0-2.1+b1 [279 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel1.83-dev amd64 1.83.0-2.1+b1 [283 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libboost-graph-parallel-dev amd64 1.83.0.2+b2 [3728 B] Get: 188 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-2.1+b1 [261 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 190 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83.0 amd64 1.83.0-2.1+b1 [354 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libboost-json1.83-dev amd64 1.83.0-2.1+b1 [369 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libboost-json-dev amd64 1.83.0.2+b2 [3704 B] Get: 193 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83.0 amd64 1.83.0-2.1+b1 [464 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libboost-locale1.83-dev amd64 1.83.0-2.1+b1 [548 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libboost-locale-dev amd64 1.83.0.2+b2 [3924 B] Get: 196 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83.0 amd64 1.83.0-2.1+b1 [700 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libboost-log1.83-dev amd64 1.83.0-2.1+b1 [870 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libboost-log-dev amd64 1.83.0.2+b2 [3796 B] Get: 199 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83.0 amd64 1.83.0-2.1+b1 [506 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libboost-math1.83-dev amd64 1.83.0-2.1+b1 [548 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libboost-math-dev amd64 1.83.0.2+b2 [3796 B] Get: 202 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 50.0-2+b1 [642 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [181 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [107 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-8.1+b3 [61.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-8.1+b3 [305 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.15 [3152 B] Get: 221 http://deb.debian.org/debian unstable/main amd64 libboost-mpi1.83-dev amd64 1.83.0-2.1+b1 [289 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-dev amd64 1.83.0.2+b2 [3680 B] Get: 223 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-2.1+b1 [351 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.15 [2408 B] Get: 225 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83.0 amd64 1.83.0-2.1+b1 [435 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python1.83-dev amd64 1.83.0-2.1+b1 [239 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libboost-mpi-python-dev amd64 1.83.0.2+b2 [3712 B] Get: 228 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libboost-nowide1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libboost-nowide-dev amd64 1.83.0.2+b2 [3668 B] Get: 231 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83.0 amd64 1.83.0-2.1+b1 [248 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libboost-numpy1.83-dev amd64 1.83.0-2.1+b1 [253 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libboost-numpy-dev amd64 1.83.0.2+b2 [3644 B] Get: 234 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-2.1+b1 [345 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-2.1+b1 [373 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 237 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-2.1+b1 [379 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 247 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83.0 amd64 1.83.0-2.1+b1 [238 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libboost-random1.83-dev amd64 1.83.0-2.1+b1 [240 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libboost-random-dev amd64 1.83.0.2+b2 [3592 B] Get: 250 http://deb.debian.org/debian unstable/main amd64 libboost-regex-dev amd64 1.83.0.2+b2 [3864 B] Get: 251 http://deb.debian.org/debian unstable/main amd64 libboost-serialization-dev amd64 1.83.0.2+b2 [3832 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83.0 amd64 1.83.0-2.1+b1 [280 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace1.83-dev amd64 1.83.0-2.1+b1 [245 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libboost-stacktrace-dev amd64 1.83.0.2+b2 [3592 B] Get: 255 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 256 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 257 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 258 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83.0 amd64 1.83.0-2.1+b1 [234 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83-dev amd64 1.83.0-2.1+b1 [236 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 261 http://deb.debian.org/debian unstable/main amd64 libboost1.83-tools-dev amd64 1.83.0-2.1+b1 [1500 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 263 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83.0 amd64 1.83.0-2.1+b1 [245 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure1.83-dev amd64 1.83.0-2.1+b1 [248 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libboost-type-erasure-dev amd64 1.83.0.2+b2 [3688 B] Get: 266 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83.0 amd64 1.83.0-2.1+b1 [336 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libboost-url1.83-dev amd64 1.83.0-2.1+b1 [422 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libboost-url-dev amd64 1.83.0.2+b2 [3732 B] Get: 269 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83.0 amd64 1.83.0-2.1+b1 [434 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libboost-wave1.83-dev amd64 1.83.0-2.1+b1 [483 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libboost-wave-dev amd64 1.83.0.2+b2 [3624 B] Get: 272 http://deb.debian.org/debian unstable/main amd64 libboost-all-dev amd64 1.83.0.2+b2 [3936 B] Get: 273 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.0.7-1 [40.9 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.7-1 [36.4 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 293 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 24.0.7-1 [119 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.7-1 [8277 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.7-1 [151 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.9-1+b1 [21.3 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3+b1 [40.8 kB] Get: 310 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.4-1+b1 [5348 B] Get: 312 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-1 [181 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.7-1+b1 [875 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-1+b1 [15.8 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-1+b1 [101 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 libegl-dev amd64 1.7.0-1+b1 [19.5 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.1+dfsg-1+b1 [32.6 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-1+b2 [779 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-1+b2 [344 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-1+b2 [608 kB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-1+b2 [806 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-1+b2 [52.3 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-1+b2 [2125 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-1+b1 [5380 B] Get: 334 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b1 [219 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-5 [14.4 kB] Get: 337 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 339 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 340 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.10.0-2 [62.5 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.10.0-2 [22.4 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.25.0-1+b2 [24.8 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.6-1.2 [22.2 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.25.0-1+b2 [128 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 libjbig-dev amd64 2.1-6.1+b1 [31.4 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 liblerc-dev amd64 4.0.0+ds-4+b1 [175 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.0+dfsg-3 [1033 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.0+dfsg-3 [344 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 libopenmm-plugins amd64 8.1.0+dfsg-3 [1422 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.43-5 [360 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-4 [759 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.10+dfsg-7.2+b1 [1835 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 libqt5concurrent5t64 amd64 5.15.10+dfsg-7.2+b1 [43.7 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.10+dfsg-7.2+b1 [213 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.10+dfsg-7.2+b1 [677 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-1 [105 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-1 [104 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-1 [129 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-1 [129 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.41-2 [795 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b1 [16.2 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.10+dfsg-7.2+b1 [3444 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.10+dfsg-7.2+b1 [2385 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.10+dfsg-7.2+b1 [123 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.10-7 [2748 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.10+dfsg-7.2+b1 [123 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.10-7 [149 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5t64 amd64 5.15.10+dfsg-7.2+b1 [149 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.10+dfsg-7.2+b1 [204 kB] Get: 391 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.10+dfsg-7.2+b1 [148 kB] Get: 392 http://deb.debian.org/debian unstable/main amd64 libvulkan-dev amd64 1.3.280.0-1 [1348 kB] Get: 393 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB] Get: 394 http://deb.debian.org/debian unstable/main amd64 qt5-qmake-bin amd64 5.15.10+dfsg-7.2+b1 [1045 kB] Get: 395 http://deb.debian.org/debian unstable/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 396 http://deb.debian.org/debian unstable/main amd64 qt5-qmake amd64 5.15.10+dfsg-7.2+b1 [223 kB] Get: 397 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev-tools amd64 5.15.10+dfsg-7.2+b1 [760 kB] Get: 398 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev amd64 5.15.10+dfsg-7.2+b1 [1122 kB] Get: 399 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5-dev amd64 5.15.10+dfsg-7.2+b1 [50.7 kB] Get: 400 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 401 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 402 http://deb.debian.org/debian unstable/main amd64 libsharpyuv-dev amd64 1.4.0-0.1 [117 kB] Get: 403 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.45.3-1 [1088 kB] Get: 404 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [358 kB] Get: 405 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 406 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 407 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 408 http://deb.debian.org/debian unstable/main amd64 libwebpdecoder3 amd64 1.4.0-0.1 [204 kB] Get: 409 http://deb.debian.org/debian unstable/main amd64 libwebp-dev amd64 1.4.0-0.1 [442 kB] Get: 410 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 libtiffxx6 amd64 4.5.1+git230720-4 [149 kB] Get: 412 http://deb.debian.org/debian unstable/main amd64 libtiff-dev amd64 4.5.1+git230720-4 [462 kB] Get: 413 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 414 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 415 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 416 http://deb.debian.org/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 418 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 419 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 420 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 421 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 422 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 423 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 424 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-8 [19.5 MB] Get: 425 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 426 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 427 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.12-7 [3869 kB] Get: 428 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 429 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 430 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get: 433 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 434 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 435 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 436 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 437 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get: 438 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 439 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 440 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 441 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] 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 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.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20016 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21008 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.1-1_amd64.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../013-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../014-libedit2_3.1-20230828-1+b1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20230828-1+b1) ... Selecting previously unselected package libcbor0.10:amd64. Preparing to unpack .../015-libcbor0.10_0.10.2-1.2_amd64.deb ... Unpacking libcbor0.10:amd64 (0.10.2-1.2) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../016-libfido2-1_1.14.0-1+b2_amd64.deb ... Unpacking libfido2-1:amd64 (1.14.0-1+b2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../017-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../018-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../019-libk5crypto3_1.20.1-6+b1_amd64.deb ... 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Setting up libboost-json1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libxcb1-dev:amd64 (1.17.0-1) ... Setting up libboost-wave1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libboost-locale1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.7.1-5) ... Setting up libgbm1:amd64 (24.0.7-1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up openssh-client (1:9.7p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.7-1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up libboost-type-erasure1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.7-1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-random-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-locale-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-wave-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up dssp (4.2.2-2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-graph1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libboost-container-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-type-erasure-dev:amd64 (1.83.0.2+b2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libboost-context1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libboost-coroutine1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libqt5core5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libegl-mesa0:amd64 (24.0.7-1) ... Setting up libboost-fiber1.83-dev:amd64 (1.83.0-2.1+b1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libevent-dev (2.1.12-stable-8.1+b3) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up libqt5sql5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up cmake (3.29.3-1+b1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up libboost-coroutine-dev:amd64 (1.83.0.2+b2) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libboost-log1.83-dev (1.83.0-2.1+b1) ... Setting up libboost-json-dev:amd64 (1.83.0.2+b2) ... Setting up libboost-log-dev (1.83.0.2+b2) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libboost-fiber-dev:amd64 (1.83.0.2+b2) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up libboost-graph-dev:amd64 (1.83.0.2+b2) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libqt5dbus5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libglx-mesa0:amd64 (24.0.7-1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libqt5concurrent5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libqt5network5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5xml5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libboost-context-dev:amd64 (1.83.0.2+b2) ... Setting up libqt5test5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libibverbs-dev:amd64 (50.0-2+b1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up qtbase5-dev-tools (5.15.10+dfsg-7.2+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up python3-pyqt5.sip (12.13.0-1+b1) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libglx-dev:amd64 (1.7.0-1+b1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up libgl-dev:amd64 (1.7.0-1+b1) ... Setting up libpmix-dev:amd64 (5.0.2-3) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libvulkan-dev:amd64 (1.3.280.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libegl-dev:amd64 (1.7.0-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up python3-fs (2.4.16-4) ... Setting up libqt5gui5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-dev (3.11.8-1) ... Setting up libboost-python1.83-dev (1.83.0-2.1+b1) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up python3-scipy (1.11.4-8) ... Setting up libqt5widgets5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libqt5help5:amd64 (5.15.10-7) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up libqt5opengl5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libboost-mpi1.83.0 (1.83.0-2.1+b1) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libqt5printsupport5t64:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libboost-graph-parallel1.83.0 (1.83.0-2.1+b1) ... Setting up libqt5designer5:amd64 (5.15.10-7) ... Setting up mpi-default-bin (1.15) ... Setting up qtbase5-dev:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libboost-graph-parallel1.83-dev (1.83.0-2.1+b1) ... Setting up python3-pyqt5 (5.15.10+dfsg-1+b1) ... Setting up libboost-mpi-python1.83.0 (1.83.0-2.1+b1) ... Setting up libqt5opengl5-dev:amd64 (5.15.10+dfsg-7.2+b1) ... Setting up libboost-graph-parallel-dev (1.83.0.2+b2) ... Setting up mpi-default-dev (1.15) ... Setting up libboost-mpi1.83-dev (1.83.0-2.1+b1) ... Setting up libboost-mpi-dev (1.83.0.2+b2) ... Setting up libboost-mpi-python1.83-dev (1.83.0-2.1+b1) ... Setting up libboost-mpi-python-dev (1.83.0.2+b2) ... Setting up libboost-all-dev (1.83.0.2+b2) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-2) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package 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 dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/openstructure-2.5.0' dh_auto_configure -- -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/x86_64-linux-gnu/openmm/plugins cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/x86_64-linux-gnu/openmm/plugins .. -- The CXX compiler identification is GNU 13.2.0 -- The C compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done CMake Warning (dev) at cmake_support/OST.cmake:892 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/OST.cmake:921 (get_compiler_version) CMakeLists.txt:174 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python311 -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: unit_test_framework -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: filesystem system -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: iostreams -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: program_options -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: regex -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.31") found components: thread -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so -- Found EIGEN: /usr/include/eigen3 (Required is at least version "3.2.0") -- Found SQLITE3: /usr/lib/x86_64-linux-gnu/libsqlite3.so (Required is at least version "3.7.13") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.43") -- Found FFTW: /usr/lib/x86_64-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.5.1") -- Found OpenMM: /usr/lib/x86_64-linux-gnu/libOpenMM.so -- Searching for python module PyQt5 for /usr/bin/python3 -- Found python module PyQt5 -- Searching for python module PyQt5.sip for /usr/bin/python3 -- Found python module PyQt5.sip -- OpenStructure will be built with the following options: Install Prefix (-DPREFIX) : /usr RPath in install (-DUSE_RPATH) : OFF Info support (-DENABLE_INFO) : ON Graphical interface (-DENABLE_GUI) : ON OpenGL support (-DENABLE_GFX) : ON Shader support (-DUSE_SHADER) : OFF Numpy support (-DUSE_NUMPY) : OFF SpaceNav Device support (-DENABLE_SPNAV) : OFF OpenMM support (-DENABLE_MM) : ON OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : /usr/lib/x86_64-linux-gnu/openmm/plugins Optimize (-DOPTIMIZE) : ON Profiling support (-DPROFILE) : OFF Double Precision (-DUSE_DOUBLE_PRECISION) : OFF Compound Lib (-DCOMPOUND_LIB) : NONE TMAlign and TMScore (-DCOMPILE_TMTOOLS) : OFF Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF -- Configuring done (4.6s) -- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/openstructure-2.5.0' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.5.0 -B/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all 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[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' 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[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' 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 -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[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/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/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.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 && /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[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' 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/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/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' 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 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]: 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 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' 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 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/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/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' 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=" make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_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/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' 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 && /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 && /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/./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=" [ 0%] Built target create_stage make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' 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 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]: 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/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]: 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/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/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' 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/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 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/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/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]: 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 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/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/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 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/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]: 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/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 && /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/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' 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' 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 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 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' 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[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 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 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' 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/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/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' 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/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 && /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' 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 && /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[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 -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/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 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/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 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=" 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/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' 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/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/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/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 && /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 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 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 [ 0%] Built target ost_config_headers 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=" 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/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/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 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' 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 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 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=" 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/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 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/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 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=" [ 0%] Built target ost_base_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/./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/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' 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 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 -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build [ 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/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 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/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/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/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/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/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/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/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/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/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/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/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/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/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 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 && /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/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/./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/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/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]: 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/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_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 && /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/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 [ 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' 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/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/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/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/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/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/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/./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/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 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/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/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/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/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/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/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 [ 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 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/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/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 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/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/./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 [ 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 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/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/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 [ 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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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 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/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 [ 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/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/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/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_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/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_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/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/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/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/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/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_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/./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/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/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/./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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/./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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/./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/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/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/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 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/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/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 [ 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/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/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/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/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/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 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/./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/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/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/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/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/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/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/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/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/./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/./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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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' [ 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/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/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/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] 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/geom/src/def.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/geom/src/composite2.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/modules/geom/src/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 | ^~~~~~~~ [ 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%] 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: /build/reproducible-path/openstructure-2.5.0/modules/geom/src/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/geom/src/composite2_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/modules/geom/src/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 | ^~~~~~~~ [ 1%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /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 -Wl,-soname,libost_geom.so.2.5 -o ../../../stage/lib/libost_geom.so.2.5.0 CMakeFiles/ost_geom.dir/mat2.cc.o CMakeFiles/ost_geom.dir/mat3.cc.o CMakeFiles/ost_geom.dir/mat4.cc.o CMakeFiles/ost_geom.dir/vec3.cc.o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o CMakeFiles/ost_geom.dir/composite2.cc.o CMakeFiles/ost_geom.dir/composite3.cc.o CMakeFiles/ost_geom.dir/composite2_op.cc.o CMakeFiles/ost_geom.dir/composite3_op.cc.o CMakeFiles/ost_geom.dir/quat.cc.o CMakeFiles/ost_geom.dir/transform.cc.o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o CMakeFiles/ost_geom.dir/point_cloud.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_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_geom.so.2.5.0 ../../../stage/lib/libost_geom.so.2.5 ../../../stage/lib/libost_geom.so 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[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' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.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/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/generic_property.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/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 [ 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 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/log.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/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 [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.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_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec2.cc [ 2%] Building CXX object 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 /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec3.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.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/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/string_ref.cc 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_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat2_op.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.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/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/profile.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_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_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vecmat3_op.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/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/base/src/units.cc 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_vec4.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec4.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_vec4.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 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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 -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 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/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/wrap_geom.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.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_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat2.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.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_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat3.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.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_mat4.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat4.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat4.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.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.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_composite2.cc [ 3%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/base/src && /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 -Wl,-soname,libost_base.so.2.5 -o ../../../stage/lib/libost_base.so.2.5.0 CMakeFiles/ost_base.dir/generic_property.cc.o CMakeFiles/ost_base.dir/log.cc.o CMakeFiles/ost_base.dir/log_sink.cc.o CMakeFiles/ost_base.dir/profile.cc.o CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_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: ../../../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/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.5.0 ../../../stage/lib/libost_base.so.2.5 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 3%] Built target ost_base make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/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/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.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' [ 3%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.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_impl.cc.o -MF CMakeFiles/ost_info.dir/info_impl.cc.o.d -o CMakeFiles/ost_info.dir/info_impl.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_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/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 | ^~~~~~~~ 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_vecmat2_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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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/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 | ^~~~~~~~ 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_vec3.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_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 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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_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 /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_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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/info/src/info_impl.hh:41, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_impl.cc:37: /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/info/src/info_impl.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/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 | ^~~~~~~~ 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_vecmat4_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 | ^~~~~~~~ [ 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, from /build/reproducible-path/openstructure-2.5.0/modules/geom/pymod/export_mat2.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_mat2.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_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 | ^~~~~~~~ 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_composite2.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: /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/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 | ^~~~~~~~ /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_mat4.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/geom/pymod/export_mat4.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 | ^~~~~~~~ [ 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, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_handle.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_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/info/src/info_handle.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/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 | ^~~~~~~~ /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/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, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.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/modules/info/src/info_handle.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/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 | ^~~~~~~~ [ 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_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 | ^~~~~~~~ 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_composite2_op.cc:21: /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_composite3_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 | ^~~~~~~~ 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_op.cc:21: /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_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, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_item.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/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/info/src/info_item.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/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.hh:29, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_set.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/info/src/info_set.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/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: /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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.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/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.5.0/modules/info/src/info_verbose_visitor.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 | ^~~~~~~~ [ 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 && /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 [ 6%] 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 [ 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 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 cd /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_info.so.2.5.0 ../../../stage/lib/libost_info.so.2.5 ../../../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=" 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/data_algorithm.cc.o [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.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 -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/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_mask.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_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 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 [ 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, 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/circle_mask.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/circle_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 | ^~~~~~~~ [ 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/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/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/data.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/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/data.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/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_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 | ^~~~~~~~ /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/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_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_handle.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_handle.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.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/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 | ^~~~~~~~ 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: /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/impl/residue_impl.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_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 | ^~~~~~~~ [ 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, 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/mol/base/src/atom_base.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/atom_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 | ^~~~~~~~ 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/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: /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/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, 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_iterator.hh:30, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_iterator.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: /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_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, 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, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_mask.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent_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/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/extent.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/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, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/extent.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/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/extent.cc: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 | ^~~~~~~~ [ 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, 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, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.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/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_factory.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/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/image_handle.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/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/image_handle.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/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/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state_fw.hh:30, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_impl.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_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/img/base/src/image_impl.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: /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: /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/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/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_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/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/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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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: /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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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: /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 | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/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/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/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/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 | ^~~~~~~~ [ 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 In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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: /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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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/editor_base.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/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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/obj-x86_64-linux-gnu/stage/include/ost/img/observable.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/observable.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/list:62, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/img/observable.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/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_state/image_state_algorithm.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/paste_impl.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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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/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, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.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_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/base/src/entity_handle.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/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_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 | ^~~~~~~~ /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/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/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/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 | ^~~~~~~~ /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/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, 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.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/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/point.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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ /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/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/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_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 | ^~~~~~~~ /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/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/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 | ^~~~~~~~ /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/modules/mol/base/src/entity_view.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.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/algorithm:60, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.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/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_view.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/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_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 | ^~~~~~~~ /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/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, 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/spherical_mask.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/spherical_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 | ^~~~~~~~ [ 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/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, 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/img/base/src/mask_info_convert.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/deque:62, from /usr/include/c++/13/stack:62, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/mask_info_convert.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 | ^~~~~~~~ [ 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, 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/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.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/data_types.hh:30, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_factory.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/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, 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/src/image_state/image_state_base.hh:34, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_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_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/img/base/src/image_state/image_state_base_fw.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/image_state/image_state_base.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/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/base/src/raster_image/raster_image.cc:38: /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/base/src/raster_image/raster_image.cc: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 | ^~~~~~~~ [ 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, 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/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query.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/query.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 | ^~~~~~~~ [ 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, 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/modules/mol/base/src/query_state.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_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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/residue_base.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/residue_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 | ^~~~~~~~ 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 | ^~~~~~~~ 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/query_state.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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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/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_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 | ^~~~~~~~ /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/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/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 | ^~~~~~~~ /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/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/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/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 | ^~~~~~~~ /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/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.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/modules/mol/base/src/module_config.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/transfer_connectivity.hh: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 | ^~~~~~~~ [ 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, 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/torsion_handle.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/mol/impl/torsion_impl_fw.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/torsion_handle.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/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, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_view_wrapper.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/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/query_view_wrapper.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/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 | ^~~~~~~~ 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/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 | ^~~~~~~~ /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/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 | ^~~~~~~~ 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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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 /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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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 [ 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, 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/chain_impl.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/base/src/impl/chain_impl.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/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/connector_impl.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/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 /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 | ^~~~~~~~ /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/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_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 | ^~~~~~~~ /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/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] 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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/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_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 | ^~~~~~~~ /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/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, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/fragment_impl.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/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 | ^~~~~~~~ [ 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, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/entity_impl.cc:35: /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/mol/base/src/impl/entity_impl.cc: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/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: /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/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/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 | ^~~~~~~~ /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/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 [ 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, 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/impl/residue_impl.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/base/src/impl/residue_impl.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/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/residue_impl.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 | ^~~~~~~~ [ 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, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/torsion_impl.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 | ^~~~~~~~ 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, 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/impl/torsion_impl.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/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, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/src/impl/surface_impl.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/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 | ^~~~~~~~ [ 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] 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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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: /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/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, 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/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_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/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: /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/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/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 /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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: /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 /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: /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 | ^~~~~~~~ [ 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, 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/gaussian.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/modules/img/alg/src/gaussian.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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ /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, 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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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, 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_gradient_magnitude.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_gradient_magnitude.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/modules/img/alg/src/gaussian_gradient_magnitude.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/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_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 | ^~~~~~~~ /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/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_laplacian.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/gaussian_laplacian.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/modules/img/alg/src/gaussian_laplacian.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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ [ 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, 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/local_sigma_threshold.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.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/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/local_sigma_threshold.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/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/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_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 | ^~~~~~~~ /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/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/normalizer.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer.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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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 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/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat.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_min_max.hh:30, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/normalizer_factory.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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.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/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/stat_min_max.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/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 | ^~~~~~~~ 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/normalizer_impl.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 | ^~~~~~~~ [ 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, 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/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 | ^~~~~~~~ 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/normalizer_impl.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/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/modules/img/alg/src/norm_od.hh:28, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/norm_od.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/img/normalizer_impl.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 | ^~~~~~~~ [ 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, 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/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_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 | ^~~~~~~~ [ 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, 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_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 | ^~~~~~~~ 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/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: /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: /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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ 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=" In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/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/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 | ^~~~~~~~ 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, 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_mirror.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/alg_mirror.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/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: /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: /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/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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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, 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: /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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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/modules/img/alg/src/transformation_base.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.hh:31, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.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/message.hh:29, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/transformations.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 | ^~~~~~~~ [ 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, 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_impl.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/vector:62, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/impl/sequence_impl.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 | ^~~~~~~~ [ 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/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/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 | ^~~~~~~~ /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/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/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_average.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/img/alg/src/line_average.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/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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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: /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 | ^~~~~~~~ [ 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, 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/modules/seq/base/src/sequence_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/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_handle.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 | ^~~~~~~~ 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/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: /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/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_region.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.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/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/aligned_region.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/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/seq/aligned_region.hh:27: /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{ | ^~~~~~~~ /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/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/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 | ^~~~~~~~ /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/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 | ^~~~~~~~ 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_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 | ^~~~~~~~ /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/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 | ^~~~~~~~ [ 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/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: /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: /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/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/views_from_sequences.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.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/obj-x86_64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/seq/base/src/views_from_sequences.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/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 | ^~~~~~~~ [ 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 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[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 /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.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/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.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu' make -f 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' [ 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/db/src/CMakeFiles/ost_db.dir/extract_data_helper.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 [ 24%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.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/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 [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.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/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 [ 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 CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/db/src/binary_container.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: /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h: In function 'void NWDP_SE(bool**, double**, double**, double**, int, int, double, double, int*, int)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:275:9: warning: unused variable 'int_min' [-Wunused-variable] 275 | int int_min=L*(gap_open-1); | ^~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NW.h:287:9: warning: unused variable 'k' [-Wunused-variable] 287 | int k=0; | ^ In file included from /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:9: /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'int NWalign_main(const char*, const char*, int, int, std::string&, std::string&, int, int*, int, int)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:41: warning: array subscript has type 'char' [-Wchar-subscripts] 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; | ~~~~~~~~^ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:415:52: warning: array subscript has type 'char' [-Wchar-subscripts] 415 | else S[i][j]=BLOSUM[seqx[i-1]][seqy[j-1]]; | ~~~~~~~~^ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h: In function 'void get_seqID(const std::string&, const std::string&, std::string&, double&, int&)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:458:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 458 | for (int i=0;i >&, char*, char*, std::vector >, std::vector >, std::vector, std::vector, int, int)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/NWalign.h:697:14: warning: statement has no effect [-Wunused-value] 697 | for (i;i::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"]) /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1607:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] 1607 | else if (atom_site_pos==_atom_site["Cartn_y"]) /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1610:43: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'std::map, int>::mapped_type' {aka 'int'} [-Wsign-compare] 1610 | else if (atom_site_pos==_atom_site["Cartn_z"]) /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1653:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1653 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1655 | for (i=1;i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1716 | for (int p=0;p >&, const std::vector >&, std::string, std::string, int, int, double, int, double, double, double)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:1855:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1855 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1857 | for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2162 | if (!mm_opt) for (i=1;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2372 | for (i=1;i >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:3289:12: warning: variable 'Lnorm_d0' set but not used [-Wunused-but-set-variable] 3289 | double Lnorm_d0; | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h: In function 'int CPalign_main(double**, double**, const char*, const char*, const char*, const char*, double*, double (*)[3], double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, std::string&, std::string&, std::string&, double&, int&, double&, double&, double&, int&, int&, int, int, std::vector >, double, double, int, int, bool, bool, bool, int, double)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/TMalign.h:3467:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3467 | for (i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3572 | for (i=0;i::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3606 | for (r=0;r >&, double, double, bool, bool, int, bool, int, int, int*, int)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/se.h:52:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 52 | for (int r=0;r::size_type' {aka 'long unsigned int'} [-Wsign-compare] 222 | for (int r=0;r 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; | ^~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:441:12: warning: unused variable 'TMmax' [-Wunused-variable] 441 | double TMmax =0; | ^~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void clear_full_PDB_lines(std::vector > >, std::string)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:670:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (chain_i=0;chain_i >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 673 | for (a=0;a >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 687 | for (a=0;a >&, int, int, int, std::string, int, double**, const std::string&)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:1010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1010 | for (a=0;a > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, std::vector > >&, std::vector > >&, int*, int*, std::vector >&)': /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; | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h: In function 'void MMalign_dimer(double&, const std::vector > >&, const std::vector > >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, double**, double**, char*, char*, char*, char*, int, int, int, int, double**, std::vector > >&, std::vector > >&, int*, int*, std::vector >&, double, bool)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2680:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2680 | for (c=0;c > >&, std::vector >&, std::vector&, std::vector >&, std::vector&, const std::string&, std::string)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:2979:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 2979 | for (c=0;c >&, const std::vector >&, double**, int*)': /build/reproducible-path/openstructure-2.5.0/modules/bindings/src/USalign/MMalign.h:3016:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 3016 | for (i=0;i 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: /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/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: /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: /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/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, 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/db/extract_data_helper.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/db/src/extract_data_helper.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/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/db/extract_data_helper.hh: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/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{ | ^~~~~~~~ /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/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/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 | ^~~~~~~~ /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/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/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/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/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/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 | ^~~~~~~~ /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/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, 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/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/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 | ^~~~~~~~ /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/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/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, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, 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/seq/impl/sequence_list_impl_fw.hh:27: 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:27: /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/string:42: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 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, 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/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 | ^~~~~~~~ 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 | ^~~~~~~~ /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/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] 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/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/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 | ^~~~~~~~ /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/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 | ^~~~~~~~ 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 [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/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/subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/subst_weight_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, 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/impl/align_impl.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/local_align.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/seq/alg/src/local_align.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/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, 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/impl/align_impl.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/semiglobal_align.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/seq/alg/src/semiglobal_align.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 | ^~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_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/variance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/variance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.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: /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/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/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/merge_pairwise_alignments.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/alg/src/merge_pairwise_alignments.cc:21: /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/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 | ^~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.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/hmm_pseudo_counts.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.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/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/sequence_similarity.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/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 | ^~~~~~~~ /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/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 | ^~~~~~~~ /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: /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/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 | ^~~~~~~~ /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/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/processor.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 | ^~~~~~~~ [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.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/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/conop.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.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_base.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib_base.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib_base.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.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/minimal_compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/minimal_compound_lib.cc 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/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.cc [ 25%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.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/diag.cc.o -MF CMakeFiles/ost_conop.dir/diag.cc.o.d -o CMakeFiles/ost_conop.dir/diag.cc.o -c /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.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/seq/alg/src/variance_map.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/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/variance_map.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/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/variance_map.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 | ^~~~~~~~ [ 25%] 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 /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.cc: In static member function 'static ost::seq::alg::ContextProfileDBPtr ost::seq::alg::ContextProfileDB::FromCRF(const String&)': /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.cc:146:56: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 146 | if(boost::iequals(".gz", boost::filesystem::extension(filename))) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_pseudo_counts.cc:4: /usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ 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' [ 25%] Built target _ost_info [ 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, 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/amino_acids.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/amino_acids.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/stl_tree.h:63, from /usr/include/c++/13/set:62, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/amino_acids.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 | ^~~~~~~~ /build/reproducible-path/openstructure-2.5.0/modules/conop/src/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/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/conop/src/conop.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/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/heuristic.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_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 | ^~~~~~~~ /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/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/hmm_score.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/seq/alg/src/hmm_score.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/seq/profile_handle.hh:27, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh: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/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, 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_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 | ^~~~~~~~ /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/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.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/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/diag.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/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/compound_lib_base.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/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 | ^~~~~~~~ /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/conop/src/rule_based.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/conop/src/rule_based.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 | ^~~~~~~~ [ 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, 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/modules/conop/src/model_check.hh:4, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/model_check.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/modules/conop/src/model_check.cc:2: /build/reproducible-path/openstructure-2.5.0/modules/conop/src/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_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/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/compound_lib.hh:27, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.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/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/openstructure-2.5.0/modules/conop/src/compound_lib.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 | ^~~~~~~~ [ 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, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/complex:45, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/base.hh:24: 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = bool; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/reproducible-path/openstructure-2.5.0/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 [ 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/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/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 | ^~~~~~~~ /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_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 /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 | ^~~~~~~~ /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_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: /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_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/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/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 | ^~~~~~~~ /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 '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, 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: /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: /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/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_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 | ^~~~~~~~ /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, 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_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 | ^~~~~~~~ /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_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/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 | ^~~~~~~~ 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_group.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/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/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/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 | ^~~~~~~~ /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/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/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 | ^~~~~~~~ /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/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/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_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 | ^~~~~~~~ /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/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/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 /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 | ^~~~~~~~ /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/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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/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_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 | ^~~~~~~~ /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/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/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 | ^~~~~~~~ [ 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/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 /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 | ^~~~~~~~ /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/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 /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 | ^~~~~~~~ /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/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/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 /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 | ^~~~~~~~ /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/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/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_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 | ^~~~~~~~ /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/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/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_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 /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 | ^~~~~~~~ /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/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 | ^~~~~~~~ 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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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: /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/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_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/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 | ^~~~~~~~ /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/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/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/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: /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/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 | ^~~~~~~~ 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: /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/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/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 | ^~~~~~~~ /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/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/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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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 | ^~~~~~~~ [ 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/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_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 | ^~~~~~~~ /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 | ^~~~~~~~ [ 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/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_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/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: /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/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/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 | ^~~~~~~~ [ 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 [ 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_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 /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 | ^~~~~~~~ /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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/distance_rmsd_test.cc:2: /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/distance_rmsd_test.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/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/mol/alg/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:3: /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 | ^~~~~~~~ [ 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, 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/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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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/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 | ^~~~~~~~ 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_query.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/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/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/superpose_frames.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/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/alg/src/superpose_frames.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/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.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/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 | ^~~~~~~~ /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 -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/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 | ^~~~~~~~ [ 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, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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, 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/pdbize.hh:22, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.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_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/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/pdbize.hh: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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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, 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/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/adjacency_bitmap.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/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.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 | ^~~~~~~~ [ 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, 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/contact_overlap.cc:2: /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/contact_overlap.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/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/contact_overlap.cc:3: /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/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 | ^~~~~~~~ /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/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_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 | ^~~~~~~~ [ 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, 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/obj-x86_64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.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 | ^~~~~~~~ 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/boost/thread/exceptions.hpp:20, from /usr/include/boost/thread/pthread/thread_data.hpp:10, from /usr/include/boost/thread/thread_only.hpp:17, from /usr/include/boost/thread/thread.hpp:12, from /usr/include/boost/thread.hpp:13, from /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/domain_find.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/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/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 /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 | ^~~~~~~~ /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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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: /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 | ^~~~~~~~ [ 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, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /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_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' [ 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::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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/mol/entity_view.hh:27: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/13/ios:42: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /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/editor_base.hh:27, from /build/reproducible-path/openstructure-2.5.0/modules/mol/base/pymod/wrap_mol.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/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 | ^~~~~~~~ /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 | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/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: /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: /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/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/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 | ^~~~~~~~ [ 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/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 | ^~~~~~~~ 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_property_mapper.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 | ^~~~~~~~ [ 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/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 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:266:17: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 266 | if (_M_string_length > _S_local_capacity) | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function '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]', 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/basic_string.h:900:24: warning: '*(std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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:877:18, 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, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.5.0/obj-x86_64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.5.0/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/13/bits/char_traits.h:358:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /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/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 | ^~~~~~~~ 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/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 | ^~~~~~~~ /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/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