Diff of the two buildlogs: -- --- b1/build.log 2025-08-28 17:44:56.541113211 +0000 +++ b2/build.log 2025-08-28 17:46:21.657218812 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Sep 30 12:06:08 -12 2026 -I: pbuilder-time-stamp: 1790813168 +I: Current time: Fri Aug 29 07:44:58 +14 2025 +I: pbuilder-time-stamp: 1756403098 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2296336/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/139546/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Aug 28 17:45 /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/139546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/139546/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='1ff533f1f2364d9ab380abe2fbd9a35a' - 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='2296336' - PS1='# ' - PS2='> ' + INVOCATION_ID=7bb465cf1fe14baa8c3982bb736e1f87 + 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=139546 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.1Ede15zR/pbuilderrc_74gD --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.1Ede15zR/b1 --logfile b1/build.log kalign_3.4.0-1.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.1Ede15zR/pbuilderrc_W9By --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.1Ede15zR/b2 --logfile b2/build.log kalign_3.4.0-1.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 codethink03-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 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2296336/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/139546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -168,7 +200,7 @@ Get: 58 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 debhelper all 13.25 [937 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 29.2 MB in 0s (115 MB/s) +Fetched 29.2 MB in 0s (151 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.) @@ -423,7 +455,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kalign-3.4.0/ && 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 > ../kalign_3.4.0-1_source.changes +I: user script /srv/workspace/pbuilder/139546/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/139546/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kalign-3.4.0/ && 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 > ../kalign_3.4.0-1_source.changes dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.4.0-1 dpkg-buildpackage: info: source distribution unstable @@ -474,7 +510,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (1.5s) +-- Configuring done (2.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -497,104 +533,104 @@ make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" -make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 1%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -[ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -[ 4%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +[ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +[ 2%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 4%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 5%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 5%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -MF CMakeFiles/bpm_utest.dir/src/alphabet.c.o.d -o CMakeFiles/bpm_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -[ 6%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 8%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -[ 9%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +[ 10%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +[ 12%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -MF CMakeFiles/tldevel.dir/src/tldevel.c.o.d -o CMakeFiles/tldevel.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 10%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +[ 9%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +[ 13%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +[ 14%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 16%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -MF CMakeFiles/task_utest.dir/src/tldevel.c.o.d -o CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 12%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -[ 13%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -[ 14%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 16%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -MF CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -MF CMakeFiles/bpm_utest.dir/src/alphabet.c.o.d -o CMakeFiles/bpm_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +[ 20%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bpm.c -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -MF CMakeFiles/edist_utest.dir/src/tldevel.c.o.d -o CMakeFiles/edist_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 21%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -MF CMakeFiles/tldevel.dir/src/tlrng.c.o.d -o CMakeFiles/tldevel.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c -[ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +[ 22%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm_test.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bpm_test.c -[ 20%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -[ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 24%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 28%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -MF CMakeFiles/edist_utest.dir/src/tlrng.c.o.d -o CMakeFiles/edist_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -[ 22%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -MF CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c +[ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong 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-Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -MF CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -[ 25%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -[ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -[ 28%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 33%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_EDIST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -MF CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o.d -o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -MF CMakeFiles/task_utest.dir/src/tlrng.c.o.d -o CMakeFiles/task_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c: In function 'main': /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c:58:15: warning: unused variable 'd2' [-Wunused-variable] 58 | float d2; | ^~ -[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -MF CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c -[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.c -[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c -[ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DTASKWRITETEST -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/task_utest.dir/src/task.c.o -MF CMakeFiles/task_utest.dir/src/task.c.o.d -o CMakeFiles/task_utest.dir/src/task.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/task.c [ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_io.c -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c [ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o @@ -607,172 +643,172 @@ cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -MF CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c [ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -MF CMakeFiles/kalign_OBJ.dir/src/task.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/task.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/task.c +[ 47%] Linking C static library libtldevel.a +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -MF CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 /build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 94 | fscanf( f_ptr, "%d", &n_tasks); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -MF CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -MF CMakeFiles/kalign_OBJ.dir/src/bpm.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bpm.c -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -MF CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c -[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +/usr/bin/ranlib libtldevel.a +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 51%] Built target tldevel +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -MF CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c [ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -[ 54%] Linking C executable task_utest -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_param.c [ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_run.c -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d CMakeFiles/task_utest.dir/src/tldevel.c.o CMakeFiles/task_utest.dir/src/tlrng.c.o CMakeFiles/task_utest.dir/src/task.c.o -o task_utest -lm -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 56%] Built target task_utest [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c -[ 59%] Linking C executable edist_utest -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC 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CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c +[ 62%] Linking C executable task_utest +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d CMakeFiles/edist_utest.dir/src/tldevel.c.o CMakeFiles/edist_utest.dir/src/tlrng.c.o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -o edist_utest -lm -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' [ 66%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -[ 67%] Linking C executable alphabet_utest -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c -[ 68%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/task_utest.dir/link.d CMakeFiles/task_utest.dir/src/tldevel.c.o CMakeFiles/task_utest.dir/src/tlrng.c.o CMakeFiles/task_utest.dir/src/task.c.o -o task_utest -lm +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 66%] Built target task_utest +[ 67%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -MF CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c -[ 68%] Built target edist_utest +[ 68%] Linking C executable alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +[ 70%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/alphabet_utest.dir/link.d CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 68%] Built target alphabet_utest -[ 70%] Linking C executable bpm_utest -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -[ 71%] Linking C static library libtldevel.a -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d CMakeFiles/bpm_utest.dir/src/tldevel.c.o CMakeFiles/bpm_utest.dir/src/tlrng.c.o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o CMakeFiles/bpm_utest.dir/src/alphabet.c.o CMakeFiles/bpm_utest.dir/src/bpm.c.o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -o bpm_utest -lm +[ 70%] Built target alphabet_utest +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/edist_utest.dir/link.d CMakeFiles/edist_utest.dir/src/tldevel.c.o CMakeFiles/edist_utest.dir/src/tlrng.c.o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -o edist_utest -lm make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 -[ 71%] Built target bpm_utest -/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -/usr/bin/ranlib libtldevel.a +[ 70%] Built target edist_utest +[ 71%] Linking C executable bpm_utest +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 71%] Built target tldevel +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/bpm_utest.dir/link.d CMakeFiles/bpm_utest.dir/src/tldevel.c.o CMakeFiles/bpm_utest.dir/src/tlrng.c.o CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o CMakeFiles/bpm_utest.dir/src/alphabet.c.o CMakeFiles/bpm_utest.dir/src/bpm.c.o CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -o bpm_utest -lm make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' [ 71%] Built target kalign_OBJ make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build +[ 71%] Built target bpm_utest +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 74%] Linking C static library libkalign.a -[ 74%] Linking C static library libkalign_static.a -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake +[ 72%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +[ 74%] Linking C static library libkalign_static.a +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 -/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -/usr/bin/ranlib libkalign_static.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' /usr/bin/ar qc libkalign.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 74%] Built target kalign_static [ 74%] Built target kalign -make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/depend -make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend +make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src 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tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -MF CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o.d -o CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_test.c -[ 90%] Linking C executable kalign_io_test -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 -[ 91%] Linking C executable kalign_cmp_test +[ 83%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src/CMakeFiles/kalign-bin.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/tests 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src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/build +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 86%] Linking C executable kalign_cmp_test cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/build +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 87%] Building C object src/CMakeFiles/kalign-bin.dir/parameters.c.o +[ 89%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c +[ 90%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP 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../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' [ 93%] Linking C executable kalign_lib_test @@ -780,25 +816,22 @@ [ 93%] Built target kalign_cmp_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 93%] Built target kalign_io_test -[ 94%] Linking C executable kalign -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 -[ 95%] Linking C executable largebench -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +[ 94%] Linking C executable kalignfmt +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 +[ 94%] Built target kalign_io_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 97%] Linking C executable kalignfmt -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -[ 97%] Built target kalign-bin -[ 97%] Built target kalign_lib_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 94%] Built target kalign_lib_test +[ 94%] Built target kalignfmt +[ 95%] Linking C executable kalign +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' -[ 97%] Built target largebench -[ 97%] Built target kalignfmt +[ 97%] Linking C executable largebench +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +[ 97%] Built target kalign-bin /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:10:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 10 | "GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE", @@ -812,12 +845,15 @@ /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:13:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 13 | "MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable kaligncpp -cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 -[100%] Linking C executable dssim +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/largebench.dir/link.d CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[ 98%] Linking C executable dssim cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 +[ 98%] Built target largebench /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dssim.dir/link.d CMakeFiles/dssim.dir/dssim_test.c.o CMakeFiles/dssim.dir/dssim.c.o -o dssim ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' +[100%] Linking CXX executable kaligncpp +cd /build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 [100%] Built target dssim /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kaligncpp.dir/link.d CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/aarch64-linux-gnu/14/libgomp.so /usr/lib/aarch64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' @@ -915,7 +951,7 @@ 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-10-01 00:06:34] : LOG : Testing correctness of serial bpm. +1: [2025-08-28 17:45:32] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -1048,63 +1084,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2026-10-01 00:06:34] : LOG : Check for correctness. -3: [2026-10-01 00:06:34] : LOG : Timing serial -3: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -4: 972 279 664 549 11 -4: 707 246 631 954 183 -4: 81 186 431 168 522 -4: 449 703 903 630 772 -4: 119 989 333 198 352 -4: 585 665 549 57 564 -4: 138 289 10 803 249 -4: 903 267 665 561 850 -4: 850 448 65 816 417 -4: 229 258 320 371 43 -4: 56 253 341 889 330 -4: 847 759 326 810 113 -4: 139 570 298 499 522 -4: 867 835 94 77 900 -4: 712 85 86 393 750 -4: 682 981 298 260 963 -4: 820 253 932 239 321 -4: 607 338 976 827 658 -4: 20 919 707 608 580 -4: 479 310 162 261 325 -4: 189 971 98 505 871 -4: 892 99 14 520 856 -4: 962 565 309 21 241 -4: 444 810 771 245 188 -4: 788 2 398 147 667 -4: 14 243 356 524 561 -4: 894 53 347 700 793 -4: 429 63 281 772 729 -4: 404 946 764 767 77 -4: 218 558 360 920 527 -4: 745 608 439 647 435 -4: 528 753 425 522 632 -4: 878 368 146 95 417 -4: 506 944 367 894 628 -4: 966 860 496 321 651 -4: 412 191 886 959 983 -4: 858 841 595 145 267 -4: 615 342 593 159 258 -4: 370 90 392 416 663 -4: 735 5 577 288 529 -4: 91 600 328 374 846 -4: 912 330 283 810 139 -4: 326 10 929 784 479 -4: 415 296 480 811 810 -4: 110 970 745 107 446 -4: 728 924 463 988 649 -4: 850 346 806 754 49 -4: 427 805 537 167 563 -4: 842 605 542 537 146 -4: 528 537 259 689 687 -4: 975 288 469 196 154 -4: 335 797 441 436 421 -4: 813 697 537 940 594 -4: 133 97 959 704 14 +3: [2025-08-28 17:45:32] : LOG : Check for correctness. +3: [2025-08-28 17:45:32] : LOG : Timing serial +3: [2025-08-28 17:45:32] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +4: 272 538 821 627 361 +4: 526 695 187 129 286 +4: 698 977 928 670 607 +4: 286 686 634 148 169 +4: 495 24 19 879 850 +4: 818 940 550 667 996 +4: 109 770 104 405 984 +4: 876 816 153 867 707 +4: 100 164 789 205 270 +4: 843 669 982 995 158 +4: 820 40 276 683 857 +4: 360 755 352 186 530 +4: 796 380 646 946 612 +4: 525 761 107 804 569 +4: 446 388 662 381 560 +4: 500 346 709 276 529 +4: 231 193 797 556 553 +4: 421 798 560 830 793 +4: 195 144 978 662 251 +4: 143 512 280 298 654 +4: 822 303 673 313 731 +4: 556 965 982 498 562 +4: 545 843 922 752 438 +4: 866 87 712 153 574 +4: 538 369 54 175 836 +4: 308 480 975 841 440 +4: 913 277 56 142 744 +4: 883 599 475 810 878 +4: 494 942 397 12 365 +4: 16 618 837 835 878 +4: 53 309 130 901 575 +4: 902 16 707 226 741 +4: 767 877 641 177 592 +4: 255 806 530 658 254 +4: 400 477 54 721 326 +4: 512 538 421 58 48 +4: 585 640 373 296 48 +4: 837 160 792 367 50 +4: 565 805 952 892 345 +4: 845 944 405 323 949 +4: 327 524 611 828 857 +4: 637 934 859 369 622 +4: 120 633 508 442 85 +4: 827 147 260 589 62 +4: 216 38 177 195 29 +4: 697 595 333 555 349 +4: 301 833 587 154 358 +4: 156 719 378 19 815 +4: 724 527 597 644 440 +4: 552 655 213 132 796 +4: 629 334 542 297 316 +4: 635 11 950 536 693 +4: 635 641 309 440 851 +4: 215 461 614 749 984 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK @@ -1126,15 +1162,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -6: [2026-10-01 00:06:34] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -6: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-10-01 00:06:34] : LOG : Building guide tree. -6: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-10-01 00:06:34] : LOG : Aligning -6: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +6: [2025-08-28 17:45:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances +6: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-08-28 17:45:32] : LOG : Building guide tree. +6: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-08-28 17:45:32] : LOG : Aligning +6: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -1163,15 +1199,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -7: [2026-10-01 00:06:34] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -7: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-10-01 00:06:34] : LOG : Building guide tree. -7: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-10-01 00:06:34] : LOG : Aligning -7: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +7: [2025-08-28 17:45:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances +7: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-08-28 17:45:32] : LOG : Building guide tree. +7: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-08-28 17:45:32] : LOG : Aligning +7: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -1200,15 +1236,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -8: [2026-10-01 00:06:34] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -8: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-10-01 00:06:34] : LOG : Building guide tree. -8: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-10-01 00:06:34] : LOG : Aligning -8: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +8: [2025-08-28 17:45:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances +8: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-08-28 17:45:32] : LOG : Building guide tree. +8: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-08-28 17:45:32] : LOG : Aligning +8: [2025-08-28 17:45:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1249,15 +1285,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -9: [2026-10-01 00:06:34] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -9: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-10-01 00:06:34] : LOG : Building guide tree. -9: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-10-01 00:06:34] : LOG : Aligning -9: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +9: [2025-08-28 17:45:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances +9: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-08-28 17:45:32] : LOG : Building guide tree. +9: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-08-28 17:45:32] : LOG : Aligning +9: [2025-08-28 17:45:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1298,15 +1334,45 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -10: [2026-10-01 00:06:34] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -10: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-10-01 00:06:34] : LOG : Building guide tree. -10: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-10-01 00:06:34] : LOG : Aligning -10: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +10: [2025-08-28 17:45:32] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances +10: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-08-28 17:45:32] : LOG : Building guide tree. +10: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-08-28 17:45:32] : LOG : Aligning +11: +11: Kalign (3.4.0) +11: +11: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann +11: +11: This program comes with ABSOLUTELY NO WARRANTY; for details type: +11: `kalign -showw'. +11: This is free software, and you are welcome to redistribute it +11: under certain conditions; consult the COPYING file for details. +11: +11: Please cite: +11: Lassmann, Timo. +11: "Kalign 3: multiple sequence alignment of large data sets." +11: Bioinformatics (2019) +11: https://doi.org/10.1093/bioinformatics/btz795 +11: +11: [2025-08-28 17:45:32] : LOG : Detected protein sequences. +11: [2025-08-28 17:45:32] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-08-28 17:45:32] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-08-28 17:45:32] : LOG : Calculating pairwise distances + 1/12 Test #2: alphabet_utest ................... Passed 0.03 sec + 2/12 Test #3: edist_utest ...................... Passed 0.03 sec + 3/12 Test #4: task_utest ....................... Passed 0.03 sec + 4/12 Test #5: C++Lib ........................... Passed 0.03 sec + 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.02 sec + 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.02 sec + 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.02 sec + 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.02 sec +10: [2025-08-28 17:45:32] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +12: [2025-08-28 17:45:32] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-08-28 17:45:32] : LOG : Protein alignments - 20 seq 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1331,42 +1397,12 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- -11: -11: Kalign (3.4.0) -11: -11: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -11: -11: This program comes with ABSOLUTELY NO WARRANTY; for details type: -11: `kalign -showw'. -11: This is free software, and you are welcome to redistribute it -11: under certain conditions; consult the COPYING file for details. -11: -11: Please cite: -11: Lassmann, Timo. -11: "Kalign 3: multiple sequence alignment of large data sets." -11: Bioinformatics (2019) -11: https://doi.org/10.1093/bioinformatics/btz795 -11: -11: [2026-10-01 00:06:34] : LOG : Detected protein sequences. -11: [2026-10-01 00:06:34] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-10-01 00:06:34] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-10-01 00:06:34] : LOG : Calculating pairwise distances -11: [2026-10-01 00:06:34] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2026-10-01 00:06:34] : LOG : Building guide tree. -12: [2026-10-01 00:06:34] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-10-01 00:06:34] : LOG : Protein alignments - 20 seq - 1/12 Test #2: alphabet_utest ................... Passed 0.04 sec - 2/12 Test #3: edist_utest ...................... Passed 0.04 sec - 3/12 Test #4: task_utest ....................... Passed 0.03 sec - 4/12 Test #5: C++Lib ........................... Passed 0.03 sec - 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.03 sec - 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.03 sec - 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.03 sec - 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.02 sec - 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.02 sec -11: [2026-10-01 00:06:34] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 -11: [2026-10-01 00:06:34] : LOG : Aligning -11: [2026-10-01 00:06:34] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 + 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec +11: [2025-08-28 17:45:32] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 +11: [2025-08-28 17:45:32] : LOG : Building guide tree. +11: [2025-08-28 17:45:32] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 +11: [2025-08-28 17:45:32] : LOG : Aligning +11: [2025-08-28 17:45:32] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -1675,41 +1711,41 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec +10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.11 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2026-10-01 00:06:34] : LOG : Testing correctness of AVX bpm. +1: [2025-08-28 17:45:32] : LOG : Testing correctness of AVX bpm. +12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% 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[==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-10-01 00:06:40] : LOG : Protein alignments - 1000 seq -1: [2026-10-01 00:06:41] : LOG : 1.559765 - dyn -1: [2026-10-01 00:06:41] : LOG : 0.000000 - bpm -1: [2026-10-01 00:06:41] : LOG : 0.096246 - bpm_block2 -1: [2026-10-01 00:06:41] : LOG : 0.089852 - bpm_block -11/12 Test #1: bpm_utest ........................ Passed 7.15 sec +1: [2025-08-28 17:45:38] : LOG : Timing DYN 256 +1: [2025-08-28 17:45:39] : LOG : 1.561129 - dyn +1: [2025-08-28 17:45:39] : LOG : 0.000000 - bpm +1: [2025-08-28 17:45:39] : LOG : 0.096818 - bpm_block2 +1: [2025-08-28 17:45:39] : LOG : 0.089981 - bpm_block +11/12 Test #1: bpm_utest ........................ Passed 7.27 sec 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-10-01 00:06:54] : LOG : Protein alignments - 10000 seq +12: [2025-08-28 17:45:48] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2026-10-01 00:07:05] : LOG : DNA alignments - 20 seq +12: [2025-08-28 17:45:56] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 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[==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-10-01 00:07:26] : LOG : DNA alignments - 1000 seq +12: [2025-08-28 17:46:02] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-10-01 00:07:38] : LOG : DNA alignments - 10000 seq +12: [2025-08-28 17:46:08] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 71.56 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 40.05 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 71.58 sec +Total Test time (real) = 40.09 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -1772,12 +1808,14 @@ 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/139546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/139546/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/2296336 and its subdirectories -I: Current time: Wed Sep 30 12:07:55 -12 2026 -I: pbuilder-time-stamp: 1790813275 +I: removing directory /srv/workspace/pbuilder/139546 and its subdirectories +I: Current time: Fri Aug 29 07:46:20 +14 2025 +I: pbuilder-time-stamp: 1756403180