Diff of the two buildlogs: -- --- b1/build.log 2024-01-11 01:23:39.411152183 +0000 +++ b2/build.log 2024-01-11 01:36:43.847737872 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 11 19:40:24 -12 2025 -I: pbuilder-time-stamp: 1739346024 +I: Current time: Thu Jan 11 15:23:42 +14 2024 +I: pbuilder-time-stamp: 1704936222 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -26,49 +26,81 @@ dpkg-source: info: unpacking shasta_0.11.1-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1783257/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Jan 11 01:23 /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/2713161/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(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=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='03eb61ba854845ee8f0d21f530ce21d0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1783257' - PS1='# ' - PS2='> ' + INVOCATION_ID=8aa0648fe887450693e9ac0486719425 + 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=2713161 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3sTbz1Mp/pbuilderrc_C8it --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3sTbz1Mp/b1 --logfile b1/build.log shasta_0.11.1-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.3sTbz1Mp/pbuilderrc_fg8U --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3sTbz1Mp/b2 --logfile b2/build.log shasta_0.11.1-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -126,15 +158,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 11 01:23 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -154,7 +186,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/1783257/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -501,7 +533,7 @@ Get: 273 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 274 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 275 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] -Fetched 152 MB in 2s (95.0 MB/s) +Fetched 152 MB in 9s (17.7 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 ... 18148 files and directories currently installed.) @@ -1375,8 +1407,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Feb 12 07:41:06 UTC 2025. -Universal Time is now: Wed Feb 12 07:41:06 UTC 2025. +Local time is now: Thu Jan 11 01:24:57 UTC 2024. +Universal Time is now: Thu Jan 11 01:24:57 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpcre3:amd64 (2:8.39-15) ... @@ -1644,7 +1676,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/shasta-0.11.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.11.1-1_source.changes +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/shasta-0.11.1/ && 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 > ../shasta_0.11.1-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.11.1-1 dpkg-buildpackage: info: source distribution unstable @@ -1705,7 +1741,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.11.1 -B/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1718,47 +1754,45 @@ make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.11.1 /build/reproducible-path/shasta-0.11.1/dynamicLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' -make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build +make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' -[ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -[ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -[ 1%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Align4.cpp cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Align4.cpp -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Alignment.cpp -[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Alignment.cpp -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Align4.cpp -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp -[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -[ 6%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o +[ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +[ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o -MF 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-DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerAlign4.cpp In file included from /usr/include/c++/12/bits/char_traits.h:46, from /usr/include/c++/12/string:40, from /build/reproducible-path/shasta-0.11.1/src/string.hpp:4, @@ -1823,54 +1855,54 @@ /build/reproducible-path/shasta-0.11.1/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ -[ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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+1950,14 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ -[ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp -[ 21%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o +[ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. 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‘p.shasta::LocalAssemblyGraphEdge::edgeId’ was declared here 1521 | typename Config::edge_property_type p; | ^ -[ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF 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/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerHttpServer-MarkerGraph.cpp [ 26%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp +[ 26%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Mode3.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerOptions.cpp +[ 45%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerReadGraph.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, @@ -2096,26 +2122,10 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o 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-MF CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalReadGraph.cpp -[ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.cpp -[ 50%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LowHash0.cpp -[ 50%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash1.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LowHash1.cpp -[ 51%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ConsensusCaller.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, @@ -2148,38 +2158,18 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [18, 9223372036854775807] and 17 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY 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/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LongBaseSequence.cpp +[ 47%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblerReads.cpp +[ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LowHash0.cpp +[ 47%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MemoryMappedAllocator.cpp -[ 56%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MemoryMappedVector.cpp -[ 56%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalAlignmentCandidateGraph.cpp -[ 57%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion 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-Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MultithreadedObject.cpp -[ 57%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalAssemblyGraph.cpp -[ 58%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MurmurHash2.cpp -[ 58%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PeakFinder.cpp -[ 59%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalMarkerGraph-Write.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2202,10 +2192,8 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PhasingGraph.cpp -[ 60%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/PngImage.cpp +[ 49%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2217,39 +2205,147 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 61%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o +[ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat 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-Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/AssemblyPathGraph.cpp +[ 50%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MemoryMappedAllocator.cpp +[ 52%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MultithreadedObject.cpp +[ 52%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/MurmurHash2.cpp +[ 53%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o -MF 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ReadLoader.cpp -[ 62%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o +[ 56%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Reads.cpp -[ 62%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o +[ 56%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ReferenceOverlapMap.cpp -[ 63%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o -c 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ConsensusCaller.cpp +[ 62%] 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/computeRunLengthRepresentation.cpp +[ 63%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Coverage.cpp +[ 64%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/Histogram.cpp +[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/diploidBayesianPhase.cpp +[ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/dset64Test.cpp +[ 65%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o +cd 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp +[ 70%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-PathGraph.cpp +[ 71%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3.cpp +[ 72%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -MF 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CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/platformDependent.cpp +[ 72%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalAssemblyGraph.cpp +[ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d 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/build/reproducible-path/shasta-0.11.1/src/shastaLapack.cpp +[ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/testSpoa.cpp +[ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/testSubsetGraph.cpp In file included from /usr/include/c++/12/ios:40, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/shasta-0.11.1/src/iostream.hpp:4, from /build/reproducible-path/shasta-0.11.1/src/Base.hpp:14, - from /build/reproducible-path/shasta-0.11.1/src/ShortBaseSequence.hpp:5, - from /build/reproducible-path/shasta-0.11.1/src/Kmer.hpp:5, - from /build/reproducible-path/shasta-0.11.1/src/Marker.hpp:21, - from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.hpp:8, - from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:2: + from /build/reproducible-path/shasta-0.11.1/src/LongBaseSequence.hpp:5, + from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph.hpp:19, + from /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.hpp:11, + from /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.cpp:2: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:2171:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(size_type, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1928:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, __cxx11::basic_string<_CharT, _Traits, _Allocator>&&) [with _CharT = char; _Traits = char_traits; _Alloc = allocator]’ at /usr/include/c++/12/bits/basic_string.h:3541:36, - inlined from ‘std::string shasta::AssemblyGraph2Edge::pathId(uint64_t) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.hpp:180:26, - inlined from ‘void shasta::AssemblyGraph2::Superbubble::writeGraphviz(std::ostream&, const shasta::AssemblyGraph2&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:4103:41: + inlined from ‘std::string shasta::CompressedAssemblyGraphEdge::gfaId() const’ at /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.cpp:400:34: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/timestamp.cpp +In file included from /usr/include/c++/12/ios:40, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from /build/reproducible-path/shasta-0.11.1/src/iostream.hpp:4, + from /build/reproducible-path/shasta-0.11.1/src/Base.hpp:14, + from /build/reproducible-path/shasta-0.11.1/src/ShortBaseSequence.hpp:5, + from /build/reproducible-path/shasta-0.11.1/src/Kmer.hpp:5, + from /build/reproducible-path/shasta-0.11.1/src/Marker.hpp:21, + from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.hpp:8, + from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:2: In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2257,35 +2353,62 @@ inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(size_type, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1928:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, __cxx11::basic_string<_CharT, _Traits, _Allocator>&&) [with _CharT = char; _Traits = char_traits; _Alloc = allocator]’ at /usr/include/c++/12/bits/basic_string.h:3541:36, inlined from ‘std::string shasta::AssemblyGraph2Edge::pathId(uint64_t) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.hpp:180:26, - inlined from ‘void shasta::AssemblyGraph2::Superbubble::writeGraphviz1(std::ostream&, const shasta::AssemblyGraph2&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:4177:41: + inlined from ‘void shasta::AssemblyGraph2::Superbubble::writeGraphviz(std::ostream&, const shasta::AssemblyGraph2&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:4103:41: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 63%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ShortBaseSequence.cpp -In file included from /usr/include/c++/12/ios:40, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from /build/reproducible-path/shasta-0.11.1/src/iostream.hpp:4, - from /build/reproducible-path/shasta-0.11.1/src/Base.hpp:14, - from /build/reproducible-path/shasta-0.11.1/src/LongBaseSequence.hpp:5, - from /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph.hpp:19, - from /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.hpp:11, - from /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.cpp:2: +[ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/touchMemory.cpp In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:2171:19, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::insert(size_type, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1928:22, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator> std::operator+(const _CharT*, __cxx11::basic_string<_CharT, _Traits, _Allocator>&&) [with _CharT = char; _Traits = char_traits; _Alloc = allocator]’ at /usr/include/c++/12/bits/basic_string.h:3541:36, - inlined from ‘std::string shasta::CompressedAssemblyGraphEdge::gfaId() const’ at /build/reproducible-path/shasta-0.11.1/src/CompressedAssemblyGraph.cpp:400:34: + inlined from ‘std::string shasta::AssemblyGraph2Edge::pathId(uint64_t) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.hpp:180:26, + inlined from ‘void shasta::AssemblyGraph2::Superbubble::writeGraphviz1(std::ostream&, const shasta::AssemblyGraph2&) const’ at /build/reproducible-path/shasta-0.11.1/src/AssemblyGraph2.cpp:4177:41: /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/SimpleBayesianConsensusCaller-Builtin.cpp -[ 64%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/SimpleBayesianConsensusCaller.cpp +[ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph-Write.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalMarkerGraph-Write.cpp +[ 76%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalMarkerGraph.cpp +[ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o +cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalReadGraph.cpp +In file included from /usr/include/c++/12/istream:39, + from /usr/include/c++/12/sstream:38, + from /usr/include/c++/12/complex:45, + from /usr/include/boost/detail/container_fwd.hpp:98, + from /usr/include/boost/container_hash/extensions.hpp:22, + from /usr/include/boost/container_hash/hash.hpp:761, + from /usr/include/boost/functional/hash.hpp:6, + from /usr/include/boost/unordered/unordered_set.hpp:18, + from /usr/include/boost/unordered_set.hpp:17, + from /usr/include/boost/graph/adjacency_list.hpp:20, + from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.hpp:29, + from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:1: +In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, + inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:51: +/usr/include/c++/12/ostream:246:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] + 246 | { return _M_insert(__p); } + | ~~~~~~~~~^~~~~ +In file included from /usr/include/boost/graph/adjacency_list.hpp:255: +In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, + inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:803:18: +/usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here + 1966 | delete su; + | ^~~~~~~~~ +In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, + inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:64: +/usr/include/c++/12/ostream:246:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] + 246 | { return _M_insert(__p); } + | ~~~~~~~~~^~~~~ +In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, + inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:804:18: +/usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here + 1966 | delete su; + | ^~~~~~~~~ In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, inlined from ‘static constexpr 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++/12/bits/basic_string.h:423:21, inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, @@ -2319,60 +2442,6 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o -MF 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CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3.cpp -[ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/performanceLog.cpp -[ 73%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/platformDependent.cpp -[ 74%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/runCommandWithTimeout.cpp -[ 75%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LocalReadGraph.cpp -[ 75%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/shastaLapack.cpp -[ 76%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/testSpoa.cpp -[ 76%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/testSubsetGraph.cpp -[ 77%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/timestamp.cpp -[ 77%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -I/build/reproducible-path/shasta-0.11.1/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/touchMemory.cpp [ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/LongBaseSequence.cpp [ 77%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o @@ -2413,39 +2482,6 @@ cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/SHASTA_ASSERT.cpp [ 86%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/ShortBaseSequence.cpp -In file included from /usr/include/c++/12/istream:39, - from /usr/include/c++/12/sstream:38, - from /usr/include/c++/12/complex:45, - from /usr/include/boost/detail/container_fwd.hpp:98, - from /usr/include/boost/container_hash/extensions.hpp:22, - from /usr/include/boost/container_hash/hash.hpp:761, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_set.hpp:18, - from /usr/include/boost/unordered_set.hpp:17, - from /usr/include/boost/graph/adjacency_list.hpp:20, - from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.hpp:29, - from /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:1: -In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, - inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:51: -/usr/include/c++/12/ostream:246:25: warning: pointer ‘v1’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] - 246 | { return _M_insert(__p); } - | ~~~~~~~~~^~~~~ -In file included from /usr/include/boost/graph/adjacency_list.hpp:255: -In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, - inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:803:18: -/usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here - 1966 | delete su; - | ^~~~~~~~~ -In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits]’, - inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:806:64: -/usr/include/c++/12/ostream:246:25: warning: pointer ‘v2’ may be used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] - 246 | { return _M_insert(__p); } - | ~~~~~~~~~^~~~~ -In function ‘void boost::remove_vertex(typename Config::vertex_descriptor, adj_list_impl&) [with Derived = adjacency_list; Config = detail::adj_list_gen, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config; Base = bidirectional_graph_helper_with_property, listS, setS, bidirectionalS, shasta::mode3::ExpandedJaccardGraphVertex, no_property, no_property, listS>::config>]’, - inlined from ‘void shasta::mode3::ExpandedJaccardGraph::merge(boost::adjacency_list::vertex_descriptor, boost::adjacency_list::vertex_descriptor, std::set >&, bool)’ at /build/reproducible-path/shasta-0.11.1/src/mode3-JaccardGraph.cpp:804:18: -/usr/include/boost/graph/detail/adjacency_list.hpp:1966:5: note: call to ‘void operator delete(void*, std::size_t)’ here - 1966 | delete su; - | ^~~~~~~~~ [ 86%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/SimpleBayesianConsensusCaller-Builtin.cpp [ 87%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o @@ -2481,8 +2517,8 @@ [ 94%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-LocalAssemblyGraph.cpp [ 94%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -[ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PathGraph.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3-PathGraph.cpp +[ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/mode3.cpp [ 95%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o cd /build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.11.1 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.11.1/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.11.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -g0 -O3 -mcx16 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o -c /build/reproducible-path/shasta-0.11.1/src/performanceLog.cpp @@ -2563,7 +2599,7 @@ make[2]: Leaving directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' # Move shared library into sphinx documentation folder for doc generation find . -name "shasta.so" -exec cp {} docs/PythonApi/ \; -cp: './docs/PythonApi/shasta.so' and 'docs/PythonApi/shasta.so' are the same file +cp: './docs/PythonApi/shasta.so' ja 'docs/PythonApi/shasta.so' on üks ja sama fail PYTHONPATH=docs/PythonApi/ python3 -m sphinx -N -bhtml docs/PythonApi/ build/html # HTML generator Running Sphinx v5.3.0 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). @@ -2594,7 +2630,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/shasta-0.11.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/reproducible-path/shasta-0.11.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.11.1 -B/build/reproducible-path/shasta-0.11.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2896,11 +2932,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.11.1-1_all.deb'. -dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.11.1-1_amd64.deb'. -dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.11.1-1_amd64.deb'. dpkg-deb: building package 'shasta' in '../shasta_0.11.1-1_amd64.deb'. +dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.11.1-1_amd64.deb'. +dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.11.1-1_amd64.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.11.1-1_amd64.deb'. +dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.11.1-1_all.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.11.1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.11.1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2908,12 +2944,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2713161/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1783257 and its subdirectories -I: Current time: Tue Feb 11 19:46:56 -12 2025 -I: pbuilder-time-stamp: 1739346416 +I: removing directory /srv/workspace/pbuilder/2713161 and its subdirectories +I: Current time: Thu Jan 11 15:36:43 +14 2024 +I: pbuilder-time-stamp: 1704937003