Diff of the two buildlogs: -- --- b1/build.log 2025-08-27 20:41:52.599607056 +0000 +++ b2/build.log 2025-08-27 20:44:45.919837837 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 27 08:38:21 -12 2025 -I: pbuilder-time-stamp: 1756327101 +I: Current time: Wed Sep 30 17:04:54 +14 2026 +I: pbuilder-time-stamp: 1790737494 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -28,53 +28,85 @@ dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1066009/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2093828/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 Sep 30 03:05 /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/2093828/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2093828/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='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='432909371fb948eb8a5e051aaa5b3fed' - 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='1066009' - PS1='# ' - PS2='> ' + INVOCATION_ID=a2d8d5c16fe94f83afdf104d85173e7b + 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=2093828 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.w9pUqF6N/pbuilderrc_Spse --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.w9pUqF6N/b1 --logfile b1/build.log hinge_0.5.0-7.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.w9pUqF6N/pbuilderrc_gynw --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.w9pUqF6N/b2 --logfile b2/build.log hinge_0.5.0-7.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1066009/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2093828/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -399,7 +431,7 @@ Get: 253 http://deb.debian.org/debian forky/main arm64 python3-pysam arm64 0.23.0+ds-1+b1 [3417 kB] Get: 254 http://deb.debian.org/debian forky/main arm64 python3-pbcore all 2.1.2+dfsg-11 [2831 kB] Get: 255 http://deb.debian.org/debian forky/main arm64 python3-ujson arm64 5.10.0-1+b4 [25.1 kB] -Fetched 229 MB in 2s (138 MB/s) +Fetched 229 MB in 1s (273 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19969 files and directories currently installed.) @@ -1228,8 +1260,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Aug 27 20:39:15 UTC 2025. -Universal Time is now: Wed Aug 27 20:39:15 UTC 2025. +Local time is now: Wed Sep 30 03:05:27 UTC 2026. +Universal Time is now: Wed Sep 30 03:05:27 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1453,7 +1485,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hinge-0.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hinge_0.5.0-7_source.changes +I: user script /srv/workspace/pbuilder/2093828/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2093828/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hinge-0.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hinge_0.5.0-7_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-7 dpkg-buildpackage: info: source distribution unstable @@ -1562,7 +1598,7 @@ to work with policies introduced by or earlier. --- Configuring done (1.1s) +-- Configuring done (0.7s) CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy @@ -1634,56 +1670,56 @@ make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake "--color=" make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake "--color=" -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build +make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build +make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -[ 3%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +[ 6%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o [ 6%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/align.c +[ 13%] Generating hinge.1 +[ 13%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +[ 17%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 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bin/lib/CMakeFiles/ini.dir/ini.c.o -[ 13%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o -[ 20%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/ini.c cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DB.c -[ 24%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DW_banded.c -[ 31%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -[ 31%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c +[ 20%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/ini.c +[ 24%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o +[ 27%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c +[ 31%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DW_banded.c +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/align.c /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); @@ -1694,22 +1730,24 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Linking C static library libPAF.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +[ 34%] Linking C static library libPAF.a cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake [ 34%] Built target man cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 -[ 37%] Linking C static library libDW_banded.a -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +[ 34%] Built target PAF +[ 37%] Linking C static library libDW_banded.a +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -[ 37%] Built target PAF [ 37%] Built target DW_banded +[ 41%] Linking C static library libkmer_lookup.a +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] 533 | free(reads); @@ -1719,8 +1757,6 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ -[ 41%] Linking C static library libkmer_lookup.a -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a @@ -1734,8 +1770,10 @@ make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/falcon.c -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': [ 48%] Linking C static library libfalcon.a +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object] 1587 | free(seq); | ^~~~~~~~~ @@ -1744,8 +1782,6 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' @@ -1757,8 +1793,8 @@ /usr/bin/ranlib libini.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' [ 55%] Linking C static library libDB.a -[ 55%] Built target ini cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake +[ 55%] Built target ini cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 /usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o /usr/bin/ranlib libDB.a @@ -1795,44 +1831,44 @@ [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/filter /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/filter /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/maximal /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake "--color=" +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/layout /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/layout /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build -[ 68%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +[ 68%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/maximal/maximal.cpp +[ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/filter/filter.cpp +[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' +make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu' -[ 75%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -[ 75%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/maximal/maximal.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/filter/filter.cpp -[ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -[ 82%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o +[ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o +[ 79%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_GRAPH_NO_LIB -DBOOST_REGEX_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp +cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp [ 86%] Linking CXX executable consensus cd /build/reproducible-path/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/consensus.dir/link.d CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a @@ -1977,12 +2013,14 @@ 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/2093828/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2093828/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/1066009 and its subdirectories -I: Current time: Wed Aug 27 08:41:51 -12 2025 -I: pbuilder-time-stamp: 1756327311 +I: removing directory /srv/workspace/pbuilder/2093828 and its subdirectories +I: Current time: Wed Sep 30 17:07:45 +14 2026 +I: pbuilder-time-stamp: 1790737665