Diff of the two buildlogs: -- --- b1/build.log 2024-12-14 07:29:46.551725259 +0000 +++ b2/build.log 2024-12-14 07:34:11.003762084 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 13 19:05:37 -12 2024 -I: pbuilder-time-stamp: 1734159937 +I: Current time: Sat Jan 17 03:52:47 +14 2026 +I: pbuilder-time-stamp: 1768571567 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: unpacking shasta_0.12.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3127883/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/383358/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 16 13:52 /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/383358/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/383358/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c52299e45a0941238aac37195784967d' - 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='3127883' - PS1='# ' - PS2='> ' + INVOCATION_ID=a566cc46fb1d484c8b8b1fb7afb22510 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=383358 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.fth8zhIW/pbuilderrc_pqVF --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fth8zhIW/b1 --logfile b1/build.log shasta_0.12.0-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.fth8zhIW/pbuilderrc_stNM --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fth8zhIW/b2 --logfile b2/build.log shasta_0.12.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3127883/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/383358/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -452,7 +484,7 @@ Get: 306 http://deb.debian.org/debian trixie/main amd64 patchelf amd64 0.18.0-1.1 [97.1 kB] Get: 307 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.6-1 [204 kB] Get: 308 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] -Fetched 224 MB in 10s (21.5 MB/s) +Fetched 224 MB in 5s (41.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) @@ -1446,8 +1478,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Dec 14 07:11:50 UTC 2024. -Universal Time is now: Sat Dec 14 07:11:50 UTC 2024. +Local time is now: Fri Jan 16 13:54:33 UTC 2026. +Universal Time is now: Fri Jan 16 13:54:33 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2+b2) ... @@ -1734,7 +1766,11 @@ 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_0.12.0-1_source.changes +I: user script /srv/workspace/pbuilder/383358/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/383358/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_0.12.0-1_source.changes dpkg-buildpackage: info: source package shasta dpkg-buildpackage: info: source version 0.12.0-1 dpkg-buildpackage: info: source distribution unstable @@ -1775,8 +1811,8 @@ -- BUILD_NATIVE is OFF -- BUILD_DEBUG is OFF -- BUILD_ID is: 0.12.0 --- Configuring done (3.1s) --- Generating done (0.2s) +-- Configuring done (0.5s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1795,68 +1831,112 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/depend -make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/depend -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary/CMakeFiles/shastaStaticLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make -f dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build.make dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/build +make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' +make -f staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build.make staticLibrary/CMakeFiles/shastaStaticLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[ 0%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o +[ 2%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -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 +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o +[ 4%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp +[ 4%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 3%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o +[ 5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o +[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o +[ 5%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o +[ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o +[ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o +[ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Align4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Align4.cpp -[ 2%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssembledSegment.cpp.o -[ 1%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o +[ 8%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignments.cpp.o +[ 8%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o +[ 9%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Alignment.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Alignment.cpp -[ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign.cpp.o +[ 9%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -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 +[ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp -[ 3%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Assembler.cpp.o +[ 10%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS 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+cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp cd 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o -c 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5%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o -c 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o +[ 13%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o -MF 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign1.cpp -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -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 -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp -[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o -[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o -[ 6%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o.d -o 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CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerDetangle.cpp +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -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 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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 +[ 19%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerHttpServer-ReadGraph.cpp In file included from /usr/include/c++/14/bits/char_traits.h:57, from /usr/include/c++/14/string:42, from /build/reproducible-path/shasta-0.12.0/src/string.hpp:4, @@ -1919,60 +1999,106 @@ /build/reproducible-path/shasta-0.12.0/src/AlignmentGraph.cpp:231:46: note: ‘vertex.shasta::AlignmentGraphVertex::color’ was declared here 231 | AlignmentGraphVertex vertex; | ^~~~~~ -[ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o -cd 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/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign4.cpp -[ 11%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerAssemblyGraph2.cpp +[ 20%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o.d -o 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-Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerInducedAlignments.cpp /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ -[ 12%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o -cd 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/build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp: In member function ‘bool shasta::Assembler::suppressAlignment(shasta::ReadId, shasta::ReadId, uint64_t)’: /build/reproducible-path/shasta-0.12.0/src/AssemblerAlign.cpp:1121:19: warning: conversion from ‘long int’ to ‘int’ may change value [-Wconversion] 1121 | return abs(r0 - r1) < int64_t(delta); | ~~~^~~~ -[ 12%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -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 +[ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMarkerGraphEdges.cpp +[ 29%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o -c 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMode3.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerMode3.cpp +[ 32%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerReadGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblyGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -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 +[ 37%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/CompactUndirectedGraph.cpp.o.d -o 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-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/AssemblerCompressedAssemblyGraph.cpp -[ 21%] Building CXX object 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dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/KmerCheckerFactory.cpp.o -c 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/MemoryMappedVector.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/MemoryMappedVector.cpp +[ 66%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/Mode3Assembler.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/Mode3Assembler.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, @@ -2198,182 +2340,14 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ -[ 43%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -DNDEBUG -DSHASTA_PYTHON_API -I/build/reproducible-path/shasta-0.12.0/dynamicLibrary/../src -g 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/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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/pybind11/include -MD -MT dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o -MF CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o.d -o CMakeFiles/shastaDynamicLibrary.dir/__/src/PeakFinder.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/PeakFinder.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, @@ -2401,104 +2375,166 @@ /usr/include/boost/graph/detail/adjacency_list.hpp:1521:41: note: ‘p’ declared here 1521 | typename Config::edge_property_type p; | ^ -[ 82%] Building CXX object dynamicLibrary/CMakeFiles/shastaDynamicLibrary.dir/__/src/PhasingGraph.cpp.o -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 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staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/globalMsa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/globalMsa.cpp +[ 86%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/html.cpp.o +cd 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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-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake -cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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 CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" 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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 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-x86_64-linux-gnu' -[100%] Built target shastaStaticLibrary -[100%] Linking CXX shared library shasta.so +[ 97%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/shastaLapack.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/shastaLapack.cpp +[ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o +[ 98%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSubsetGraph.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSubsetGraph.cpp +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/testSpoa.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/testSpoa.cpp +[ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/timestamp.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/timestamp.cpp +[ 99%] Building CXX object staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/c++ -DBOOST_ALLOW_DEPRECATED_HEADERS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBUILD_ID=0.12.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -MD -MT staticLibrary/CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -MF CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o.d -o CMakeFiles/shastaStaticLibrary.dir/__/src/touchMemory.cpp.o -c /build/reproducible-path/shasta-0.12.0/src/touchMemory.cpp +[ 99%] Linking CXX shared library shasta.so cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,shasta.so -o shasta.so CMakeFiles/shastaDynamicLibrary.dir/__/src/Align4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Alignment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AlignmentGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssembledSegment.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/Assembler.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o 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" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphCleanupDuplicateMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkerGraphEdges.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMarkers.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerMode3.cpp.o CMakeFiles/shastaDynamicLibrary.dir/__/src/AssemblerOptions.cpp.o 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 -lpython3.12 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' -[100%] Built target shastaDynamicLibrary +[ 99%] 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-x86_64-linux-gnu' cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-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-x86_64-linux-gnu' -[100%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o +[ 99%] Building CXX object dynamicExecutable/CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -Wall -Wconversion -Wno-unused-result -Wno-trigraphs -Wno-psabi -g0 -O3 -mcx16 -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 +[100%] Linking CXX static library shasta.a +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/staticLibrary && /usr/bin/cmake -P CMakeFiles/shastaStaticLibrary.dir/cmake_clean_target.cmake +cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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 CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign1.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign3.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign4.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlign5.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentCandidates.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignmentGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAnalyzePaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerAssemblyGraph2.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCompressedAssemblyGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerCreateReadGraphUsingPseudoPaths.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerDetangle.cpp.o "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Alignments.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-AssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-CompressedAssemblyGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph0.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-MarkerGraph1.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-ReadGraph.cpp.o" "CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer-Reads.cpp.o" CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerHttpServer.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerInducedAlignments.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerLowHash.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerConnectivityGraph.cpp.o CMakeFiles/shastaStaticLibrary.dir/__/src/AssemblerMarkerGraph.cpp.o 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 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 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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-x86_64-linux-gnu' +[100%] Built target shastaStaticLibrary [100%] Linking CXX executable shastaDynamic cd /build/reproducible-path/shasta-0.12.0/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now CMakeFiles/shastaDynamicExecutable.dir/__/srcMain/main.cpp.o -o shastaDynamic -Wl,-rpath,/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/dynamicLibrary: ../dynamicLibrary/shasta.so -latomic -lboost_system -lboost_program_options -lboost_chrono -lboost_serialization -lspoa -lpng -lz -llapack -lblas -lgfortran -lquadmath -lpthread -lpython3.12 -ldl -lm @@ -2544,7 +2580,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/shasta-0.12.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/shasta-0.12.0 -B/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2668,118 +2704,118 @@ -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/generateBandageLabelsFromAlignment.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/bin/testGlobalMsa.py -- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/PacBio-CLR-Dec2019.conf --- Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/conf/RemoveConflicts.conf +-- Installing: 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Installing: /build/reproducible-path/shasta-0.12.0/debian/tmp/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu/./shasta-install/docs/Markers.png make[1]: Leaving directory '/build/reproducible-path/shasta-0.12.0/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' @@ -2828,12 +2864,12 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged +dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'shasta.so' debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/shasta-0.12.0' # The library is in a more unusual place (nested within /usr/lib), so @@ -2850,11 +2886,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. -dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. +dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. dpkg-deb: building package 'python3-shasta' in '../python3-shasta_0.12.0-1_amd64.deb'. +dpkg-deb: building package 'shasta-dbgsym' in '../shasta-dbgsym_0.12.0-1_amd64.deb'. dpkg-deb: building package 'python3-shasta-dbgsym' in '../python3-shasta-dbgsym_0.12.0-1_amd64.deb'. -dpkg-deb: building package 'python3-shasta-doc' in '../python3-shasta-doc_0.12.0-1_all.deb'. +dpkg-deb: building package 'shasta' in '../shasta_0.12.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../shasta_0.12.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../shasta_0.12.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2862,12 +2898,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/383358/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/383358/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/3127883 and its subdirectories -I: Current time: Fri Dec 13 19:29:45 -12 2024 -I: pbuilder-time-stamp: 1734161385 +I: removing directory /srv/workspace/pbuilder/383358 and its subdirectories +I: Current time: Sat Jan 17 03:57:09 +14 2026 +I: pbuilder-time-stamp: 1768571829