Diff of the two buildlogs: -- --- b1/build.log 2025-02-11 12:20:54.814249927 +0000 +++ b2/build.log 2025-02-11 12:32:55.853802843 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 11 00:16:35 -12 2025 -I: pbuilder-time-stamp: 1739276195 +I: Current time: Tue Mar 17 08:43:58 +14 2026 +I: pbuilder-time-stamp: 1773686638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -24,52 +24,84 @@ dpkg-source: info: applying 0001-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/997254/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1023509/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Mar 16 18:44 /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/1023509/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1023509/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3a22eec9b71542ee86b3c27c36e913df' - 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='997254' - PS1='# ' - PS2='> ' + INVOCATION_ID=6a875e4301ed4ba592a9a645e70255a7 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=1023509 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.k859ezUj/pbuilderrc_2diQ --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k859ezUj/b1 --logfile b1/build.log shasta_0.12.0-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.k859ezUj/pbuilderrc_TCy3 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k859ezUj/b2 --logfile b2/build.log shasta_0.12.0-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/997254/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1023509/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -463,7 +495,7 @@ Get: 306 http://deb.debian.org/debian unstable/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 307 http://deb.debian.org/debian unstable/main arm64 sphinx-common all 8.1.3-4 [616 kB] Get: 308 http://deb.debian.org/debian unstable/main arm64 python3-sphinx all 8.1.3-4 [468 kB] -Fetched 211 MB in 1s (237 MB/s) +Fetched 211 MB in 1s (243 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:arm64. (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 ... 19920 files and directories currently installed.) @@ -1452,8 +1484,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Feb 11 12:17:20 UTC 2025. -Universal Time is now: Tue Feb 11 12:17:20 UTC 2025. +Local time is now: Mon Mar 16 18:45:51 UTC 2026. +Universal Time is now: Mon Mar 16 18:45:51 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4) ... @@ -1742,7 +1774,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shasta_0.12.0-2_source.changes +I: user script /srv/workspace/pbuilder/1023509/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/1023509/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/shasta-0.12.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../shasta_0.12.0-2_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-2 dpkg-buildpackage: info: source distribution experimental @@ -1783,7 +1819,7 @@ -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 --- Configuring done (1.2s) +-- Configuring done (1.8s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1810,53 +1846,53 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend -make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" +make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' -make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' +make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' [ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -[ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -[ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -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-0.12.0/src/AlignmentGraph.cpp -[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -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-0.12.0/src/Align4.cpp +[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -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-0.12.0/src/Alignment.cpp -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssembledSegment.cpp -[ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o +[ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/Align4.cpp +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -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-0.12.0/src/AlignmentGraph.cpp cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/Alignment.cpp -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Assembler.cpp -[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp In file included from /usr/include/c++/14/bits/exception_ptr.h:41, from /usr/include/c++/14/exception:166, from /usr/include/c++/14/ios:41, @@ -2006,18 +2046,6 @@ 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 9223372036854775801 into destination object of size [0, 9223372036854775807] allocated by ‘operator new’ -[ 18%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o -cd 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp -[ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph1.cpp -[ 20%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o -MF 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o +[ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-MarkerGraph0.cpp +[ 21%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-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/AssemblerHttpServer-MarkerGraph1.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -c 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp +[ 23%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion 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-DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-Reads.cpp +/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: +/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] + 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp +/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] + 623 | sortedEdges.push_back(make_pair(abs(residual), e)); + | ^~~~~~~~ +[ 25%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); @@ -2130,46 +2183,54 @@ /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 623 | sortedEdges.push_back(make_pair(abs(residual), e)); | ^~~~~~~~ -[ 23%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp +[ 27%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp +[ 27%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp -[ 24%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/AssemblyGraph2.cpp -[ 30%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp -[ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerLowHash.cpp +[ 35%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, @@ -2182,65 +2243,90 @@ /build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ | ^~~~~~~~~~ -/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp: In member function ‘void shasta::Assembler::exploreUndirectedReadGraph(const std::vector >&, std::ostream&)’: -/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:468:51: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] - 468 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp:623:49: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] - 623 | sortedEdges.push_back(make_pair(abs(residual), e)); - | ^~~~~~~~ +[ 35%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerConnectivityGraph.cpp -[ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o +In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, + from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, + from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, + from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, + from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: +/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: +/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] + 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); + | ~~~^~~~~~~~ +/build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ + 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ + | ^~~~~~~~~~ +/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: +/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] + 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 36%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyGraph2.cpp +[ 36%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/AssemblyGraph2.cpp +[ 37%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/AssemblyPathGraph.cpp -[ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o +[ 37%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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 CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph2.cpp -[ 33%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraph.cpp -[ 34%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o +[ 37%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblyPathGraph.cpp +[ 38%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Base.cpp -[ 34%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o +[ 39%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o.d -o 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o +[ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/HttpServer.cpp +[ 47%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o -c 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-Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp -[ 41%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion 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-I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp -[ 41%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG 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-DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerCheckerFactory.cpp +[ 49%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/KmerTable.cpp In file included from /build/reproducible-path/shasta-0.12.0/src/CompressedAssemblyGraph.cpp:2: In copy constructor ‘constexpr shasta::CompressedAssemblyGraphEdge::CompressedAssemblyGraphEdge(const shasta::CompressedAssemblyGraphEdge&)’, inlined from ‘boost::list_edge::list_edge(Vertex, Vertex, const EdgeProperty&) [with Vertex = void*; EdgeProperty = shasta::CompressedAssemblyGraphEdge]’ at /usr/include/boost/graph/detail/adjacency_list.hpp:891:19, @@ -2268,120 +2354,6 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ -[ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -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-0.12.0/src/LocalAssemblyGraph.cpp -[ 42%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/LocalMarkerGraph0-Write.cpp -[ 43%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph2.cpp -In file included from /build/reproducible-path/shasta-0.12.0/src/ReadId.hpp:5, - from /build/reproducible-path/shasta-0.12.0/src/OrientedReadPair.hpp:5, - from /build/reproducible-path/shasta-0.12.0/src/Alignment.hpp:4, - from /build/reproducible-path/shasta-0.12.0/src/Assembler.hpp:5, - from /build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:3: -/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::leastSquareAnalysis(shasta::LocalReadGraph&, std::vector&) const’: -/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:1665:22: warning: conversion from ‘__gnu_cxx::__alloc_traits, double>::value_type’ {aka ‘double’} to ‘int’ may change value [-Wfloat-conversion] - 1665 | SHASTA_ASSERT(abs(S[N-1]) < 1.e-14); - | ~~~^~~~~~~~ -/build/reproducible-path/shasta-0.12.0/src/SHASTA_ASSERT.hpp:18:37: note: in definition of macro ‘SHASTA_ASSERT’ - 18 | #define SHASTA_ASSERT(expression) ((expression) ? (static_cast(0)) : \ - | ^~~~~~~~~~ -[ 43%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerReads.cpp -/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp: In member function ‘void shasta::Assembler::flagInconsistentAlignmentsThreadFunction2(std::size_t)’: -/build/reproducible-path/shasta-0.12.0/src/AssemblerReadGraph.cpp:2051:71: warning: conversion from ‘double’ to ‘int’ may change value [-Wfloat-conversion] - 2051 | const double residual = abs((x1 - x0) - graph[e].averageAlignmentOffset); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -I/build/reproducible-path/shasta-0.12.0/staticLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/mode3-PhasingTable.cpp -[ 96%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp +[ 98%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/timestamp.cpp +[ 99%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -I/usr/include/python3.13 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp +[100%] Linking CXX static library shasta.a +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake +cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/staticLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaStaticLibrary.dir/link.txt --verbose=1 +/usr/bin/ar qc shasta.a CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerOptions.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o 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CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o +/usr/bin/ranlib shasta.a +make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' +[100%] Built target shastaStaticLibrary +[100%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" 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CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/touchMemory.cpp.o -latomic -lpng -lboost_program_options -lboost_serialization -lpthread -lz -lspoa -llapack -lblas -lpython3.13 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' -[ 99%] Built target shastaDynamicLibrary +[100%] Built target shastaDynamicLibrary make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/depend make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/shasta-0.12.0 /build/reproducible-path/shasta-0.12.0/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' make -f dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build.make dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' -[ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o +[100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicExecutable/../src -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -MD -MT dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -MF CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o.d -o CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -c /build/reproducible-path/shasta-0.12.0/srcMain/main.cpp -[ 99%] Linking CXX executable shastaDynamic +[100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/dynamicExecutable && /usr/bin/cmake -E cmake_link_script CMakeFiles/shastaDynamicExecutable.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/shasta-0.12.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyPathGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Base.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompactUndirectedGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/CompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConfigurationTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Coverage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HashedKmerChecker.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Histogram.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/HttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/InducedAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerCheckerFactory.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/KmerTable.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentCandidateGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalAssemblyGraph.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0-Write.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalMarkerGraph1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LocalReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LongBaseSequence.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/LowHash0.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MarkerGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MedianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedAllocator.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MultithreadedObject.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/MurmurHash2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PeakFinder.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PhasingGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PngImage.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/PythonModule.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReadLoader.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/Reads.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ReferenceOverlapMap.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SHASTA_ASSERT.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/ShortBaseSequence.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller-Builtin.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleBayesianConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/SimpleConsensusCaller.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/assembleMarkerGraphPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/buildId.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/compressAlignment.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/computeRunLengthRepresentation.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/diploidBayesianPhase.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/dset64Test.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/enumeratePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/extractKmer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/filesystem.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/longestPath.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/mappedCopy.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/markerAccessFunctions.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-LocalAssembly.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasedComponent.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PhasingTable.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/mode3-PrimaryGraph.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/performanceLog.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/platformDependent.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/runCommandWithTimeout.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -/usr/bin/ranlib shasta.a -make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' -[100%] Built target shastaStaticLibrary +[100%] Built target shastaDynamicExecutable make[3]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-aarch64-linux-gnu' @@ -2923,8 +2959,8 @@ dh_missing --list-missing make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0' dh_dwz -a -dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so: .debug_info section not present dwz: debian/shasta/usr/bin/shasta: .debug_info section not present +dwz: debian/python3-shasta/usr/lib/python3/dist-packages/shasta.cpython-313-aarch64-linux-gnu.so: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a @@ -2956,9 +2992,9 @@ dh_builddeb dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-2_arm64.deb'. dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-2_arm64.deb'. +dpkg-deb: building package 'shasta' in '../shasta_0.12.0-2_arm64.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-2_arm64.deb'. dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-2_all.deb'. -dpkg-deb: building package 'shasta' in '../shasta_0.12.0-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-2_arm64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2966,12 +3002,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1023509/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1023509/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/997254 and its subdirectories -I: Current time: Tue Feb 11 00:20:53 -12 2025 -I: pbuilder-time-stamp: 1739276453 +I: removing directory /srv/workspace/pbuilder/1023509 and its subdirectories +I: Current time: Tue Mar 17 08:55:54 +14 2026 +I: pbuilder-time-stamp: 1773687354