Diff of the two buildlogs: -- --- b1/build.log 2025-01-18 10:54:53.351392760 +0000 +++ b2/build.log 2025-01-18 10:58:41.705095449 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Feb 20 05:16:37 -12 2026 -I: pbuilder-time-stamp: 1771607797 +I: Current time: Sun Jan 19 00:54:57 +14 2025 +I: pbuilder-time-stamp: 1737197697 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -23,54 +23,86 @@ 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/14952/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/54803/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 18 10:55 /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/54803/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/54803/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='0defd7db529541879a367fcd5c25df4b' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='14952' - PS1='# ' - PS2='> ' + INVOCATION_ID=267bea0baf724fb08cad84f526bf5619 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=54803 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.UTrhRLxi/pbuilderrc_dub2 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UTrhRLxi/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.UTrhRLxi/pbuilderrc_qLPJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UTrhRLxi/b2 --logfile b2/build.log kalign_3.4.0-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos16-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14952/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/54803/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -170,7 +202,7 @@ Get: 58 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 debhelper all 13.23 [919 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-2 [467 kB] -Fetched 42.7 MB in 2s (24.2 MB/s) +Fetched 42.7 MB in 1s (75.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:i386. (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 ... 19837 files and directories currently installed.) @@ -425,7 +457,11 @@ 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/54803/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/54803/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 @@ -476,7 +512,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (1.4s) +-- Configuring done (4.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -490,7 +526,7 @@ -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build - cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -503,93 +539,89 @@ make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend 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-i686-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/alphabet_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/edist_utest.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-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-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build 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-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -[ 1%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -[ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -[ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -[ 8%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 8%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 12%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +[ 1%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 4%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 2%] 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/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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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-i686-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 -Wformat -Werror=format-security -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-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration 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/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 -Wformat -Werror=format-security -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/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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 10%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC 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-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 -Wformat -Werror=format-security -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 +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 18%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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/esl_stopwatch.c.o -MF CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o.d -o CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 20%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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/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 +[ 21%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 22%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 24%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 /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 +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 27%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -[ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 29%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +[ 31%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra 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^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o +[ 35%] Linking C static library libtldevel.a +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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-i686-linux-gnu' +[ 35%] Built target edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.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 -Wformat -Werror=format-security -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-i686-linux-gnu' +[ 36%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 37%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 37%] Built target alphabet_utest +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +/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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 41%] Built target tldevel +[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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_check.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_check.c -[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o +[ 44%] Linking C executable task_utest +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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_cmp.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c -[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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_sort.c.o -MF CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_sort.c -[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu' +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 48%] Built target task_utest +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 /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); @@ -628,71 +676,59 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 59%] Linking C executable bpm_utest +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +[ 70%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o +[ 71%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-i686-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 -Wformat -Werror=format-security -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 -[ 66%] Linking C executable task_utest -cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 make[3]: 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-ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.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 -Wformat -Werror=format-security -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-i686-linux-gnu' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -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-i686-linux-gnu' -[ 74%] Built target alphabet_utest -[ 74%] 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 -[ 74%] Built target edist_utest -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -[ 74%] Built target tldevel /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 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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 @@ -701,100 +737,106 @@ make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-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[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 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make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests/CMakeFiles/dssim.dir/DependInfo.cmake "--color=" +make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-i686-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 /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu 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-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i686-linux-gnu/14/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +[ 97%] Built target largebench +[ 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", @@ -808,19 +850,13 @@ /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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Built target kalign_io_test -[ 97%] Built target kalignfmt -[ 97%] Built target largebench -[ 97%] Built target kalign_cmp_test -[ 97%] Built target kalign_lib_test -[ 97%] Built target kalign-bin [ 98%] Linking C executable dssim cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.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 -Wformat -Werror=format-security -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/i686-linux-gnu/14/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' -[ 98%] Built target dssim [100%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.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 -Wformat -Werror=format-security -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/i686-linux-gnu/14/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' +[100%] Built target dssim /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/i686-linux-gnu/14/libgomp.so /usr/lib/i386-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' [100%] Built target kaligncpp @@ -828,10 +864,10 @@ /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' dh_auto_test - cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 + cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j22 +/usr/bin/ctest --force-new-ctest-process --verbose -j10 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/DartConfiguration.tcl @@ -904,20 +940,8 @@ 10: Test command: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" 10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 10: Test timeout computed to be: 1500 -test 11 - Start 11: kalign_itest_BB30014.tfa - -11: Test command: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" -11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -11: Test timeout computed to be: 1500 -test 12 - Start 12: DSSIM_takes_a_min - -12: Test command: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests/dssim -12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -12: Test timeout computed to be: 1500 1: LEN: 256 -1: [2026-02-20 17:17:04] : LOG : Testing correctness of serial bpm. +1: [2025-01-18 10:55:49] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -1050,63 +1074,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2026-02-20 17:17:04] : LOG : Check for correctness. -3: [2026-02-20 17:17:04] : LOG : Timing serial -3: [2026-02-20 17:17:04] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -4: 29 295 550 183 171 -4: 117 781 658 960 416 -4: 688 247 809 976 137 -4: 147 458 116 336 499 -4: 374 907 968 240 759 -4: 640 948 982 956 399 -4: 478 994 380 335 78 -4: 55 923 699 910 347 -4: 201 867 886 406 693 -4: 317 262 14 385 293 -4: 335 946 106 653 202 -4: 596 410 460 646 107 -4: 831 371 452 521 708 -4: 419 738 236 608 284 -4: 375 553 639 526 60 -4: 720 862 364 543 678 -4: 447 196 894 438 508 -4: 537 753 885 530 942 -4: 390 451 302 147 739 -4: 197 293 200 617 353 -4: 621 617 408 386 284 -4: 827 231 252 397 561 -4: 857 960 898 806 738 -4: 808 344 709 124 414 -4: 704 158 739 883 627 -4: 166 951 882 624 702 -4: 638 212 337 336 14 -4: 217 516 768 15 354 -4: 657 235 43 932 591 -4: 611 992 516 497 479 -4: 900 359 654 238 658 -4: 467 406 228 52 547 -4: 832 753 607 593 503 -4: 790 585 708 537 520 -4: 561 442 436 717 542 -4: 89 270 401 547 290 -4: 427 73 561 717 668 -4: 309 751 436 278 136 -4: 935 554 470 933 636 -4: 762 32 648 81 860 -4: 185 166 853 498 647 -4: 154 587 642 285 184 -4: 752 913 7 120 389 -4: 304 618 525 134 286 -4: 207 861 929 192 180 -4: 100 884 812 512 754 -4: 341 628 814 598 897 -4: 451 738 469 752 306 -4: 944 420 858 154 250 -4: 389 574 999 396 826 -4: 503 719 135 876 793 -4: 149 770 752 243 147 -4: 672 568 907 114 224 -4: 313 257 131 828 961 +3: [2025-01-18 10:55:49] : LOG : Check for correctness. +3: [2025-01-18 10:55:49] : LOG : Timing serial +3: [2025-01-18 10:55:49] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +4: 335 105 377 680 506 +4: 683 790 76 981 17 +4: 194 317 137 997 860 +4: 748 269 838 322 144 +4: 906 692 835 985 602 +4: 318 709 815 373 854 +4: 636 576 393 276 189 +4: 39 606 861 26 245 +4: 427 798 952 635 311 +4: 215 471 751 873 12 +4: 364 740 455 530 8 +4: 489 668 938 851 634 +4: 356 110 422 900 115 +4: 283 137 344 747 646 +4: 595 830 101 839 594 +4: 988 705 718 226 493 +4: 643 149 780 925 348 +4: 207 286 0 123 158 +4: 272 146 145 319 155 +4: 823 929 691 735 437 +4: 932 583 694 204 887 +4: 548 71 678 166 54 +4: 227 824 107 214 660 +4: 34 5 149 939 909 +4: 168 246 764 5 293 +4: 363 25 612 870 696 +4: 255 771 984 920 119 +4: 945 13 959 38 79 +4: 640 115 57 888 402 +4: 440 732 978 114 996 +4: 954 958 793 630 984 +4: 890 51 71 673 549 +4: 543 35 260 79 282 +4: 785 567 580 364 939 +4: 600 831 382 715 834 +4: 266 951 748 435 1 +4: 3 581 607 841 353 +4: 68 526 479 410 811 +4: 863 456 393 247 25 +4: 363 587 784 518 537 +4: 969 986 80 221 894 +4: 636 70 216 604 446 +4: 241 949 582 905 243 +4: 185 273 636 598 679 +4: 252 647 305 892 110 +4: 963 948 555 116 584 +4: 544 879 771 709 350 +4: 526 805 833 354 72 +4: 166 102 661 894 547 +4: 605 654 61 275 67 +4: 885 146 472 969 527 +4: 538 690 218 46 409 +4: 400 951 287 143 413 +4: 278 29 760 419 334 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK @@ -1128,15 +1152,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -6: [2026-02-20 17:17:04] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -6: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-02-20 17:17:04] : LOG : Building guide tree. -6: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2026-02-20 17:17:04] : LOG : Aligning -6: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +6: [2025-01-18 10:55:49] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances +6: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-01-18 10:55:49] : LOG : Building guide tree. +6: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2025-01-18 10:55:49] : LOG : Aligning +6: [2025-01-18 10:55:49] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -1165,27 +1189,12 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -7: [2026-02-20 17:17:04] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -7: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-02-20 17:17:04] : LOG : Building guide tree. -7: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2026-02-20 17:17:04] : LOG : Aligning -7: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: >1aab_ -7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG -7: KFEDMAKADKARYEREMKTYIPPKGE---------- -7: >1j46_A -7: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW -7: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK -7: >1k99_A -7: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM -7: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- -7: >2lef_A -7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA -7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK +7: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +7: [2025-01-18 10:55:49] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances +7: [2025-01-18 10:55:49] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +7: [2025-01-18 10:55:49] : LOG : Building guide tree. 8: 8: Kalign (3.4.0) 8: @@ -1202,39 +1211,10 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -8: [2026-02-20 17:17:04] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -8: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-02-20 17:17:04] : LOG : Building guide tree. -8: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2026-02-20 17:17:04] : LOG : Aligning -8: [2026-02-20 17:17:04] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -8: >1al2_ad -8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -8: KA--- -8: >1bbt_ac -8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -8: ----- -8: >1bev_ac -8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -8: TAILQ -8: >1mec_ac -8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -8: Q---- +8: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +8: [2025-01-18 10:55:49] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances 9: 9: Kalign (3.4.0) 9: @@ -1251,15 +1231,67 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -9: [2026-02-20 17:17:04] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -9: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-02-20 17:17:04] : LOG : Building guide tree. -9: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2026-02-20 17:17:04] : LOG : Aligning -9: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +9: [2025-01-18 10:55:49] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances +9: [2025-01-18 10:55:49] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2025-01-18 10:55:49] : LOG : Building guide tree. +10: +10: Kalign (3.4.0) +10: +10: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann +10: +10: This program comes with ABSOLUTELY NO WARRANTY; for details type: +10: `kalign -showw'. +10: This is free software, and you are welcome to redistribute it +10: under certain conditions; consult the COPYING file for details. +10: +10: Please cite: +10: Lassmann, Timo. +10: "Kalign 3: multiple sequence alignment of large data sets." +10: Bioinformatics (2019) +10: https://doi.org/10.1093/bioinformatics/btz795 +10: +10: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +10: [2025-01-18 10:55:49] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances + 1/12 Test #2: alphabet_utest ................... Passed 0.06 sec + 2/12 Test #3: edist_utest ...................... Passed 0.05 sec + 3/12 Test #4: task_utest ....................... Passed 0.05 sec + 4/12 Test #5: C++Lib ........................... Passed 0.04 sec + 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.04 sec +test 11 + Start 11: kalign_itest_BB30014.tfa + +11: Test command: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" +11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests +11: Test timeout computed to be: 1500 +test 12 + Start 12: DSSIM_takes_a_min + +12: Test command: /build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu/tests/dssim +12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests +12: Test timeout computed to be: 1500 +7: [2025-01-18 10:55:49] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +7: [2025-01-18 10:55:49] : LOG : Aligning +7: [2025-01-18 10:55:49] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +7: >1aab_ +7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG +7: KFEDMAKADKARYEREMKTYIPPKGE---------- +7: >1j46_A +7: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW +7: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK +7: >1k99_A +7: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM +7: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- +7: >2lef_A +7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA +7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK +9: [2025-01-18 10:55:49] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2025-01-18 10:55:49] : LOG : Aligning +9: [2025-01-18 10:55:49] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1284,31 +1316,15 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- -10: -10: Kalign (3.4.0) -10: -10: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -10: -10: This program comes with ABSOLUTELY NO WARRANTY; for details type: -10: `kalign -showw'. -10: This is free software, and you are welcome to redistribute it -10: under certain conditions; consult the COPYING file for details. -10: -10: Please cite: -10: Lassmann, Timo. -10: "Kalign 3: multiple sequence alignment of large data sets." -10: Bioinformatics (2019) -10: https://doi.org/10.1093/bioinformatics/btz795 -10: -10: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -10: [2026-02-20 17:17:04] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -10: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-02-20 17:17:04] : LOG : Building guide tree. -10: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2026-02-20 17:17:04] : LOG : Aligning -10: [2026-02-20 17:17:04] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2025-01-18 10:55:49] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 +8: [2025-01-18 10:55:49] : LOG : Building guide tree. +8: [2025-01-18 10:55:49] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2025-01-18 10:55:49] : LOG : Aligning +10: [2025-01-18 10:55:49] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +10: [2025-01-18 10:55:49] : LOG : Building guide tree. +10: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2025-01-18 10:55:49] : LOG : Aligning +10: [2025-01-18 10:55:49] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -1349,26 +1365,52 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2026-02-20 17:17:04] : LOG : Detected protein sequences. -11: [2026-02-20 17:17:04] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2026-02-20 17:17:04] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2026-02-20 17:17:04] : LOG : Calculating pairwise distances -11: [2026-02-20 17:17:04] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2026-02-20 17:17:04] : LOG : Building guide tree. - 1/12 Test #2: alphabet_utest ................... Passed 0.02 sec - 2/12 Test #3: edist_utest ...................... Passed 0.02 sec - 3/12 Test #4: task_utest ....................... Passed 0.02 sec - 4/12 Test #5: C++Lib ........................... Passed 0.02 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 - 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.02 sec -12: [2026-02-20 17:17:04] : LOG : DSSim - a simplistic sequence simulator. -12: [2026-02-20 17:17:04] : LOG : Protein alignments - 20 seq -11: [2026-02-20 17:17:04] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2026-02-20 17:17:04] : LOG : Aligning -11: [2026-02-20 17:17:04] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 +11: [2025-01-18 10:55:49] : LOG : Detected protein sequences. +11: [2025-01-18 10:55:49] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2025-01-18 10:55:49] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2025-01-18 10:55:49] : LOG : Calculating pairwise distances +12: [2025-01-18 10:55:49] : LOG : DSSim - a simplistic sequence simulator. +12: [2025-01-18 10:55:49] : LOG : Protein alignments - 20 seq + 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.06 sec + 7/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.05 sec + 8/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.04 sec +8: [2025-01-18 10:55:49] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +8: >1al2_ad +8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS +8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF +8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ +8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ +8: KA--- +8: >1bbt_ac +8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- +8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF +8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY +8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- +8: ----- +8: >1bev_ac +8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N +8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC +8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG +8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ +8: TAILQ +8: >1mec_ac +8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- +8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF +8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM +8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP +8: Q---- + 9/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.06 sec +11: [2025-01-18 10:55:49] : LOG : CPU Time: 0.07u 00:00:00.07 Elapsed: 00:00:00.00 +11: [2025-01-18 10:55:49] : LOG : Building guide tree. +11: [2025-01-18 10:55:49] : LOG : CPU Time: 0.09u 00:00:00.09 Elapsed: 00:00:00.00 +11: [2025-01-18 10:55:49] : LOG : Aligning +1: 0 6300 0 0 +1: 0 0 6300 6300 +1: 0 0 0 0 +1: 0 0 0 0 +1: +1: [2025-01-18 10:55:49] : LOG : Testing correctness of AVX bpm. +11: [2025-01-18 10:55:49] : LOG : CPU Time: 0.13u 00:00:00.13 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -1677,46 +1719,40 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -10/12 Test #11: kalign_itest_BB30014.tfa ......... 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2026-02-20 17:17:08] : LOG : Protein alignments - 1000 seq +10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.19 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 1: Dyn AVX DYN/AVX -1: [2026-02-20 17:17:10] : LOG : Timing DYN 256 -1: [2026-02-20 17:17:12] : LOG : 1.680612 - dyn -1: [2026-02-20 17:17:12] : LOG : 0.000000 - bpm -1: [2026-02-20 17:17:12] : LOG : 0.128167 - bpm_block2 -1: [2026-02-20 17:17:12] : LOG : 0.139969 - bpm_block -11/12 Test #1: bpm_utest ........................ Passed 8.47 sec +1: [2025-01-18 10:56:00] : LOG : Timing DYN 256 +1: [2025-01-18 10:56:04] : LOG : 2.365695 - dyn +1: [2025-01-18 10:56:04] : LOG : 0.000000 - bpm +1: [2025-01-18 10:56:04] : LOG : 0.231372 - bpm_block2 +1: [2025-01-18 10:56:04] : LOG : 0.239959 - bpm_block +11/12 Test #1: bpm_utest ........................ 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% +12: [2025-01-18 10:56:20] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2026-02-20 17:17:21] : LOG : Protein alignments - 10000 seq +12: [2025-01-18 10:56:47] : LOG : Protein alignments - 10000 seq 12: [ ] 0% 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Passed 43.35 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 145.46 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 43.37 sec +Total Test time (real) = 145.60 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ - cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1770,12 +1806,14 @@ 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/54803/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/54803/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/14952 and its subdirectories -I: Current time: Fri Feb 20 05:17:52 -12 2026 -I: pbuilder-time-stamp: 1771607872 +I: removing directory /srv/workspace/pbuilder/54803 and its subdirectories +I: Current time: Sun Jan 19 00:58:39 +14 2025 +I: pbuilder-time-stamp: 1737197919