Diff of the two buildlogs: -- --- b1/build.log 2025-10-08 06:40:30.868764786 +0000 +++ b2/build.log 2025-10-08 06:45:00.373078607 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 7 18:36:18 -12 2025 -I: pbuilder-time-stamp: 1759905378 +I: Current time: Wed Nov 11 03:03:30 +14 2026 +I: pbuilder-time-stamp: 1794315810 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ dpkg-source: info: unpacking kalign_3.4.0-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1362583/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2014747/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 10 13:04 /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/2014747/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2014747/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='779d0d131210409ca513b7b9277543f9' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1362583' - PS1='# ' - PS2='> ' + INVOCATION_ID=f3248d48030842dc8ee876ea5293cf0f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2014747 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.42Bpkle6/pbuilderrc_fAJ5 --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.42Bpkle6/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.42Bpkle6/pbuilderrc_zuBe --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.42Bpkle6/b2 --logfile b2/build.log kalign_3.4.0-1.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1362583/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2014747/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: 60 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 32.3 MB in 0s (137 MB/s) +Fetched 32.3 MB in 2s (15.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -433,7 +465,11 @@ 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/2014747/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2014747/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 @@ -534,7 +570,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (1.7s) +-- Configuring done (1.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -587,7 +623,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (5.6s) +-- Configuring done (2.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -643,7 +679,7 @@ -- Compiler c flags : -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -- OpenMP version : 4.5 -- OpenMP flags : -fopenmp --- Configuring done (4.2s) +-- Configuring done (3.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -657,7 +693,7 @@ -- Build files have been written to: /build/reproducible-path/kalign-3.4.0/obj-avx2 make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -683,102 +719,106 @@ cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-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/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 -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-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' -[ 5%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 5%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -[ 6%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -[ 9%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -[ 10%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -[ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -[ 12%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -[ 14%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -[ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o -[ 18%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c -[ 20%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +[ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o +[ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +[ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +[ 5%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +[ 6%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +[ 8%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o +[ 10%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +[ 10%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 13%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +[ 13%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +[ 14%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +[ 16%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 17%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +[ 20%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 22%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 20%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc 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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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 31%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +[ 22%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-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=. 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-I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 39%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o -[ 39%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -[ 20%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -[ 20%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -[ 39%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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/build/reproducible-path/kalign-3.4.0/lib/src/euclidean_dist.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -MF CMakeFiles/bpm_utest.dir/src/bpm.c.o.d -o CMakeFiles/bpm_utest.dir/src/bpm.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/bpm.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP 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lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -[ 44%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd 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-Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +[ 36%] 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Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o +[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +[ 47%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 50%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 52%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/aln_wrap.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/aln_mem.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -795,41 +835,14 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:272:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 272 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein2': -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] - 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~ -/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; - | ^~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:148:31: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (13 chars into 12 available) [-Wunterminated-string-initialization] - 148 | char DNA_letters[12]= "acgtunACGTUN"; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] - 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein2': +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] + 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_protein_BZX': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:203:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (24 chars into 23 available) [-Wunterminated-string-initialization] 203 | char aacode[23] = "ARNDCQEGHILKMFPSTWYVBZX"; @@ -846,8 +859,14 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ @@ -867,148 +886,161 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:148:31: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (13 chars into 12 available) [-Wunterminated-string-initialization] + 148 | char DNA_letters[12]= "acgtunACGTUN"; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] + 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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; + | ^~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c -[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o [ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 66%] Linking C executable alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c +[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c +[ 66%] Linking C executable bpm_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +[ 67%] Linking C static library libtldevel.a +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake +[ 68%] Linking C executable alphabet_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 -[ 67%] Linking C executable task_utest +[ 70%] Linking C executable task_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +/usr/bin/ranlib libtldevel.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu' -[ 67%] Built target kalign_OBJ +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu' +[ 70%] Built target tldevel +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu' +[ 70%] Built target alphabet_utest +[ 70%] Built target kalign_OBJ +[ 70%] Built target bpm_utest make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend -[ 67%] Built target alphabet_utest make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" +[ 70%] Built target task_utest make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build +make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 70%] Linking C static library libkalign.a -[ 70%] Linking C static library libkalign_static.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 71%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +[ 72%] Linking C static library libkalign_static.a +[ 74%] Linking C static library libkalign.a cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -[ 70%] Built target task_utest cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 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tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend -make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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'/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/kalign_lib_test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests 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tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -MF CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o.d -o CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim.c.o -MF CMakeFiles/dssim.dir/dssim.c.o.d -o CMakeFiles/dssim.dir/dssim.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim.c +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -MF CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o.d -o CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_test.c /build/reproducible-path/kalign-3.4.0/tests/dssim.c: In function 'emit_letter': /build/reproducible-path/kalign-3.4.0/tests/dssim.c:315:29: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 315 | char alphabet[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1017,26 +1049,25 @@ /build/reproducible-path/kalign-3.4.0/tests/dssim.c:321:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (5 chars into 4 available) [-Wunterminated-string-initialization] 321 | char alphabet[4] = "ACGT"; | ^~~~~~ -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 90%] Linking C executable kalign_io_test +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 +[ 91%] Linking C executable kalign_cmp_test +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [ 93%] Built target kalign_io_test -[ 93%] Built target kalign_cmp_test /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 93%] Built target kalign_lib_test -[ 94%] Linking C executable kalignfmt -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -[ 95%] Linking C executable kalign +[ 94%] Linking C executable kalign +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 95%] Linking C executable kalignfmt +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 97%] Linking C executable largebench -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 -[ 97%] Built target kalignfmt /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp: In function 'int main()': @@ -1052,19 +1083,24 @@ /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-bin +[ 95%] Built target kalignfmt +[ 95%] Built target kalign-bin +[ 95%] Built target kalign_cmp_test +[ 95%] Built target kalign_lib_test +[ 98%] Linking C executable dssim +[ 98%] Linking C executable largebench +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 97%] Built target largebench -[ 98%] Linking CXX executable kaligncpp -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 -[100%] Linking C executable dssim -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 98%] Built target largebench +[ 98%] Built target dssim +[100%] Linking CXX executable kaligncpp +cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[100%] Built target dssim [100%] Built target kaligncpp make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/CMakeFiles 0 @@ -1072,7 +1108,7 @@ debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' dh_auto_build --builddirectory obj-sse4.1 - cd obj-sse4.1 && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-sse4.1 && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-sse4.1/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-sse4.1//CMakeFiles/progress.marks @@ -1083,11 +1119,11 @@ make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend -make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' @@ -1097,103 +1133,118 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.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 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lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +[ 27%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -MF CMakeFiles/tldevel.dir/src/tlrng.c.o.d -o CMakeFiles/tldevel.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 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lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o -[ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -[ 35%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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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 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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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 -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 40%] Building C 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 41%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC 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lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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-I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/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 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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 +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o [ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 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/build/reproducible-path/kalign-3.4.0/lib/src/bisectingKmeans.c cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c +/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o +/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1210,11 +1261,15 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:272:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 272 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein2': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ +/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; + | ^~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ @@ -1234,17 +1289,6 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -/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; - | ^~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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); @@ -1279,66 +1323,58 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c -[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c +[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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Linking C executable alphabet_utest +[ 67%] Linking C executable task_utest +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 70%] Linking C static library libtldevel.a -[ 71%] Linking C executable task_utest +[ 68%] Linking C static library libtldevel.a cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +[ 70%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script 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-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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 71%] Built target task_utest -[ 71%] Built target alphabet_utest +[ 71%] Linking C executable bpm_utest +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +[ 71%] Built target kalign_OBJ [ 71%] Built target edist_utest [ 71%] Built target bpm_utest -[ 71%] Built target kalign_OBJ +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +/usr/bin/ranlib libtldevel.a make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" -/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o 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libkalign.a +[ 74%] Built target tldevel +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 @@ -1354,15 +1390,15 @@ make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend +make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend make[4]: Entering 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/build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kalign_io_test.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend +make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/dssim.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/kalign_lib_test.dir/DependInfo.cmake "--color=" make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend @@ -1375,51 +1411,51 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1 && /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-sse4.1 /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/build -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/build +make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/build make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/build make 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tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/build make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +[ 85%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o +[ 89%] Building C object tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o +[ 89%] Building C object src/CMakeFiles/kalign-bin.dir/parameters.c.o +[ 89%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o +[ 89%] Building C object 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-I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/c++ -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -MF CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o.d -o CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -c /build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp +cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c /build/reproducible-path/kalign-3.4.0/tests/dssim.c: In function 'emit_letter': /build/reproducible-path/kalign-3.4.0/tests/dssim.c:315:29: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 315 | char alphabet[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1428,36 +1464,6 @@ /build/reproducible-path/kalign-3.4.0/tests/dssim.c:321:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (5 chars into 4 available) [-Wunterminated-string-initialization] 321 | char alphabet[4] = "ACGT"; | ^~~~~~ -[ 90%] Linking C executable kalign_io_test -[ 91%] Linking C executable kalign_cmp_test -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 93%] Linking C executable kalign_lib_test -[ 93%] Built target kalign_cmp_test -[ 93%] Built target kalign_io_test -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 -[ 94%] Linking C executable kalignfmt -[ 95%] Linking C executable kalign -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 95%] Built target kalign_lib_test -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat 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object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c -[ 13%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -[ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -[ 21%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c -[ 21%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -cd 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/usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib 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lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib 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/build/reproducible-path/kalign-3.4.0/lib/src/bpm.c cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g 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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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection 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-DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 40%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +[ 43%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o +[ 43%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 44%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 47%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 47%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -DUTEST_ALPHABET -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -MF CMakeFiles/alphabet_utest.dir/src/alphabet.c.o.d -o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c +[ 48%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.c.o +[ 50%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o +[ 54%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +[ 54%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o +[ 54%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 55%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 56%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -MF CMakeFiles/bpm_utest.dir/src/tldevel.c.o.d -o CMakeFiles/bpm_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:148:31: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (13 chars into 12 available) [-Wunterminated-string-initialization] + 148 | char DNA_letters[12]= "acgtunACGTUN"; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] + 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1647,10 +1701,6 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -/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; - | ^~ /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); @@ -1658,6 +1708,22 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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; + | ^~ +[ 58%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 59%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +[ 63%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o +[ 63%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +[ 63%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 64%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1678,38 +1744,31 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:148:31: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (13 chars into 12 available) [-Wunterminated-string-initialization] - 148 | char DNA_letters[12]= "acgtunACGTUN"; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] - 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c -[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 64%] Built target kalign_OBJ +[ 66%] Linking C executable task_utest +[ 70%] Linking C executable edist_utest +[ 70%] Linking C executable bpm_utest +[ 70%] Linking C executable alphabet_utest +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +[ 70%] Built target alphabet_utest +[ 70%] Built target task_utest +[ 70%] Built target edist_utest +[ 70%] Built target bpm_utest +[ 71%] Linking C static library libtldevel.a +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 +[ 71%] Built target kalign_OBJ make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' @@ -1717,130 +1776,99 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' cd /build/reproducible-path/kalign-3.4.0/obj-avx && /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-avx /build/reproducible-path/kalign-3.4.0/obj-avx/lib 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libkalign.a -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake +[ 72%] Linking C static library libkalign_static.a cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake -[ 70%] Linking C executable bpm_utest -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpm_utest.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +[ 74%] Linking C static library libkalign.a +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +/usr/bin/ranlib libtldevel.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +[ 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 CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o 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tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.dir/depend make -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend +make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/src /build/reproducible-path/kalign-3.4.0/obj-avx/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/depend -[ 70%] Built target kalign_static +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +cd /build/reproducible-path/kalign-3.4.0/obj-avx && /usr/bin/cmake 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/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp +cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/run_reformat.c.o -MF CMakeFiles/kalignfmt.dir/run_reformat.c.o.d -o CMakeFiles/kalignfmt.dir/run_reformat.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_reformat.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalignfmt.dir/parameters.c.o -MF CMakeFiles/kalignfmt.dir/parameters.c.o.d -o CMakeFiles/kalignfmt.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c /build/reproducible-path/kalign-3.4.0/tests/dssim.c: In function 'emit_letter': /build/reproducible-path/kalign-3.4.0/tests/dssim.c:315:29: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 315 | char alphabet[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -1849,21 +1877,12 @@ /build/reproducible-path/kalign-3.4.0/tests/dssim.c:321:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (5 chars into 4 available) [-Wunterminated-string-initialization] 321 | char alphabet[4] = "ACGT"; | ^~~~~~ +[ 91%] Linking C executable kalign_cmp_test +[ 91%] Linking C executable kalign_io_test +cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 -[ 93%] Built target kalign_cmp_test -[ 93%] Built target kalign_io_test -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 93%] Built target kalign_lib_test -[ 94%] Linking C executable kalignfmt -cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -[ 95%] Linking C executable kalign -cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 97%] Linking C executable largebench -cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 /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", @@ -1877,28 +1896,45 @@ /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 kalignfmt -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +[ 94%] Linking C executable kalignfmt +cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 97%] Built target kalign-bin -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 97%] Built target largebench -[ 98%] Linking CXX executable kaligncpp -cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 -[100%] Linking C executable dssim -cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +[ 94%] Built target kalign_lib_test +[ 94%] Built target kalign_cmp_test +[ 94%] Built target kalign_io_test +[ 95%] Linking C executable kalign +[ 95%] Built target kalignfmt +cd /build/reproducible-path/kalign-3.4.0/obj-avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 +[ 97%] Linking C executable largebench +[ 98%] Linking C executable dssim +cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/dssim.dir/link.txt --verbose=1 +[100%] Linking CXX executable kaligncpp +cd /build/reproducible-path/kalign-3.4.0/obj-avx/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' [100%] Built target kaligncpp [100%] Built target dssim +[100%] Built target kalign-bin +[100%] Built target largebench make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' dh_auto_build --builddirectory obj-avx2 - cd obj-avx2 && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-avx2 && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles /build/reproducible-path/kalign-3.4.0/obj-avx2//CMakeFiles/progress.marks @@ -1910,9 +1946,9 @@ make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_OBJ.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/tldevel.dir/DependInfo.cmake "--color=" make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/bpm_utest.dir/DependInfo.cmake "--color=" @@ -1924,156 +1960,146 @@ cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/task_utest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +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[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 1%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o -[ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o -[ 4%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o -[ 5%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -[ 6%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 8%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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-DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o -MF CMakeFiles/tldevel.dir/src/tlmisc.c.o.d -o CMakeFiles/tldevel.dir/src/tlmisc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c +[ 35%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o +[ 36%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -MD -MT lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -MF CMakeFiles/bpm_utest.dir/src/tlrng.c.o.d -o CMakeFiles/bpm_utest.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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-I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -[ 35%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && 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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 +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 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/build/reproducible-path/kalign-3.4.0/lib/src/msa_io.c -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -MF CMakeFiles/kalign_OBJ.dir/src/test.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/test.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/test.c +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc 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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 +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -[ 52%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && 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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-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_protein_BZX': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:203:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (24 chars into 23 available) [-Wunterminated-string-initialization] 203 | char aacode[23] = "ARNDCQEGHILKMFPSTWYVBZX"; | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] + 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_DNA': +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:231:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (17 chars into 16 available) [-Wunterminated-string-initialization] 231 | char dnacode[16] = "ACGTUNRYSWKMBDHV"; | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein': -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:272:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] - 272 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein2': -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] - 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c: In function 'detect_alphabet': /build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:148:31: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (13 chars into 12 available) [-Wunterminated-string-initialization] 148 | char DNA_letters[12]= "acgtunACGTUN"; | ^~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] - 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf( f_ptr, "%d", &n_tasks); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': -/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] - 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_protein_BZX': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:203:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (24 chars into 23 available) [-Wunterminated-string-initialization] 203 | char aacode[23] = "ARNDCQEGHILKMFPSTWYVBZX"; | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/msa_op.c:149:36: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (41 chars into 40 available) [-Wunterminated-string-initialization] + 149 | char protein_letters[40] = "acdefghiklmnpqrstvwyACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_DNA': +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:272:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] + 272 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:231:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (17 chars into 16 available) [-Wunterminated-string-initialization] 231 | char dnacode[16] = "ACGTUNRYSWKMBDHV"; | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein2': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_reduced_protein': +/build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] + 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:272:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 272 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ @@ -2081,10 +2107,6 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_mem.c /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c: In function 'create_default_protein': /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:167:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 167 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -2105,42 +2127,57 @@ /build/reproducible-path/kalign-3.4.0/lib/src/alphabet.c:326:27: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 326 | char aacode[20] = "ACDEFGHIKLMNPQRSTVWY"; | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf( f_ptr, "%d", &n_tasks); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_setup.c -[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c +[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o [ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqseq.c +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_controller.c [ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -[ 63%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -fPIC -std=gnu11 -Wall -Wextra -pedantic -fopenmp -MD -MT lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_seqprofile.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/aln_profileprofile.c.o [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 static library libtldevel.a -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/tldevel.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/tldevel.dir/link.txt --verbose=1 -/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 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -I/build/reproducible-path/kalign-3.4.0/lib/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 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cmake_link_script CMakeFiles/edist_utest.dir/link.txt --verbose=1 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/alphabet_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 70%] Built target alphabet_utest -[ 70%] Built target bpm_utest -[ 70%] Built target edist_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 70%] Built target kalign_OBJ +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 71%] Built target alphabet_utest +[ 71%] Built target task_utest +[ 71%] Built target kalign_OBJ +[ 71%] Built target bpm_utest +[ 71%] Built target edist_utest make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/depend make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' @@ -2149,18 +2186,20 @@ cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /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-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/lib /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/CMakeFiles/kalign_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/build +make -f lib/CMakeFiles/kalign_static.dir/build.make lib/CMakeFiles/kalign_static.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 72%] Linking C static library libkalign.a -[ 72%] Linking C static library libkalign_static.a +[ 74%] Linking C static library libkalign.a +[ 74%] Linking C static library libkalign_static.a +/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 cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -P CMakeFiles/kalign.dir/cmake_clean_target.cmake -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 74%] Built target tldevel cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 -[ 74%] Linking C executable task_utest -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/task_utest.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_static.dir/link.txt --verbose=1 /usr/bin/ar qc libkalign.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o /usr/bin/ranlib libkalign.a /usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o @@ -2176,72 +2215,69 @@ make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' cd /build/reproducible-path/kalign-3.4.0/obj-avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/kalign-3.4.0 /build/reproducible-path/kalign-3.4.0/src /build/reproducible-path/kalign-3.4.0/obj-avx2 /build/reproducible-path/kalign-3.4.0/obj-avx2/src /build/reproducible-path/kalign-3.4.0/obj-avx2/src/CMakeFiles/kalignfmt.dir/DependInfo.cmake "--color=" make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/depend -make -f tests/CMakeFiles/kaligncpp.dir/build.make 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/parameters.c.o -MF CMakeFiles/kalign-bin.dir/parameters.c.o.d -o CMakeFiles/kalign-bin.dir/parameters.c.o -c /build/reproducible-path/kalign-3.4.0/src/parameters.c +[ 87%] Building C object src/CMakeFiles/kalign-bin.dir/run_kalign.c.o +[ 89%] Building C object tests/CMakeFiles/largebench.dir/large_benchmark.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/largebench.dir/large_benchmark.c.o -MF CMakeFiles/largebench.dir/large_benchmark.c.o.d -o CMakeFiles/largebench.dir/large_benchmark.c.o -c /build/reproducible-path/kalign-3.4.0/tests/large_benchmark.c cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/kalign-bin.dir/run_kalign.c.o -MF CMakeFiles/kalign-bin.dir/run_kalign.c.o.d -o CMakeFiles/kalign-bin.dir/run_kalign.c.o -c /build/reproducible-path/kalign-3.4.0/src/run_kalign.c -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cc -DHAVE_OPENMP -I/build/reproducible-path/kalign-3.4.0/lib/src -I/build/reproducible-path/kalign-3.4.0/lib/include -I/build/reproducible-path/kalign-3.4.0/obj-avx2/lib -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -std=gnu11 -Wall -Wextra -pedantic -MD -MT tests/CMakeFiles/dssim.dir/dssim_test.c.o -MF CMakeFiles/dssim.dir/dssim_test.c.o.d -o CMakeFiles/dssim.dir/dssim_test.c.o -c /build/reproducible-path/kalign-3.4.0/tests/dssim_test.c -[ 89%] Built target task_utest /build/reproducible-path/kalign-3.4.0/tests/dssim.c: In function 'emit_letter': /build/reproducible-path/kalign-3.4.0/tests/dssim.c:315:29: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (21 chars into 20 available) [-Wunterminated-string-initialization] 315 | char alphabet[20] = "ACDEFGHIKLMNPQRSTVWY"; @@ -2250,35 +2286,20 @@ /build/reproducible-path/kalign-3.4.0/tests/dssim.c:321:28: warning: initializer-string for array of 'char' truncates NUL terminator but destination lacks 'nonstring' attribute (5 chars into 4 available) [-Wunterminated-string-initialization] 321 | char alphabet[4] = "ACGT"; | ^~~~~~ -[ 90%] Linking C executable kalign_io_test -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 +[ 91%] Linking C executable kalign_io_test [ 91%] Linking C executable kalign_cmp_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_cmp_test.dir/link.txt --verbose=1 +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_io_test.dir/link.txt --verbose=1 /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_io_test.dir/link.d CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -o kalign_io_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_cmp_test.dir/link.d CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -o kalign_cmp_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 91%] Built target kalign_io_test +[ 91%] Built target kalign_cmp_test [ 93%] Linking C executable kalign_lib_test cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign_lib_test.dir/link.txt --verbose=1 -[ 93%] Built target kalign_io_test -[ 93%] Built target kalign_cmp_test [ 94%] Linking C executable kalignfmt cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalignfmt.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 95%] Linking C executable kalign -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 -[ 95%] Built target kalign_lib_test -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 97%] Linking C executable largebench -[ 97%] Built target kalignfmt -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 97%] Built target kalign-bin -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /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", @@ -2292,26 +2313,41 @@ /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 largebench -[100%] Linking CXX executable kaligncpp -[100%] Linking C executable dssim +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalignfmt.dir/link.d CMakeFiles/kalignfmt.dir/run_reformat.c.o CMakeFiles/kalignfmt.dir/parameters.c.o -o kalignfmt ../lib/libtldevel.a ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 94%] Built target kalignfmt +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign_lib_test.dir/link.d CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o -o kalign_lib_test ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 95%] Linking C executable kalign +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/kalign-bin.dir/link.txt --verbose=1 +[ 97%] Linking C executable largebench +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/largebench.dir/link.txt --verbose=1 +[ 98%] Linking CXX executable kaligncpp cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/kaligncpp.dir/link.txt --verbose=1 -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +[ 98%] Built target kalign_lib_test +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/kalign-bin.dir/link.d "CMakeFiles/kalign-bin.dir/run_kalign.c.o" "CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[100%] Built target dssim +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 98%] Built target largebench +[ 98%] Built target kalign-bin /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[100%] Linking C executable dssim [100%] Built target kaligncpp +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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/x86_64-linux-gnu/15/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[100%] Built target dssim make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/kalign-3.4.0/obj-avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_auto_test - cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j40 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -2397,7 +2433,7 @@ 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-10-08 06:37:31] : LOG : Testing correctness of serial bpm. +1: [2026-11-10 13:04:54] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -2530,63 +2566,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2025-10-08 06:37:31] : LOG : Check for correctness. -3: [2025-10-08 06:37:31] : LOG : Timing serial -3: [2025-10-08 06:37:31] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -4: 969 892 202 59 859 -4: 747 257 165 732 348 -4: 261 477 714 449 765 -4: 171 269 614 230 719 -4: 183 705 736 142 879 -4: 562 988 861 166 877 -4: 336 220 983 446 974 -4: 387 57 372 223 551 -4: 641 816 370 542 125 -4: 77 273 807 565 543 -4: 500 65 641 657 890 -4: 811 192 781 713 208 -4: 423 835 615 3 497 -4: 899 449 871 969 434 -4: 116 741 846 777 463 -4: 638 478 24 966 645 -4: 734 271 557 249 780 -4: 496 249 790 394 269 -4: 580 917 803 40 129 -4: 191 53 796 128 644 -4: 540 637 266 455 530 -4: 703 19 238 575 345 -4: 81 431 90 444 355 -4: 538 186 347 82 853 -4: 649 789 195 390 977 -4: 518 331 718 906 533 -4: 876 629 322 468 323 -4: 349 41 130 297 210 -4: 48 290 554 508 328 -4: 475 347 559 267 659 -4: 887 547 503 265 260 -4: 673 685 635 771 555 -4: 233 240 373 348 279 -4: 695 96 120 144 941 -4: 825 12 378 268 734 -4: 917 572 125 984 152 -4: 242 553 874 212 309 -4: 196 512 546 748 306 -4: 136 34 526 588 705 -4: 478 21 627 10 386 -4: 480 793 739 157 941 -4: 878 830 664 555 945 -4: 40 905 322 375 502 -4: 829 655 312 581 178 -4: 599 860 913 594 40 -4: 914 733 86 313 994 -4: 327 787 657 770 617 -4: 688 4 620 66 510 -4: 199 164 330 558 591 -4: 24 859 524 267 724 -4: 866 938 887 743 75 -4: 49 272 724 539 54 -4: 238 27 64 433 657 -4: 852 697 875 391 988 +3: [2026-11-10 13:04:54] : LOG : Check for correctness. +3: [2026-11-10 13:04:54] : LOG : Timing serial +3: [2026-11-10 13:04:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +4: 843 632 177 755 380 +4: 79 763 998 242 764 +4: 478 52 760 134 604 +4: 832 301 932 211 889 +4: 234 619 592 125 883 +4: 406 416 947 218 783 +4: 749 595 850 389 138 +4: 373 590 372 866 7 +4: 121 679 616 179 625 +4: 797 515 920 844 673 +4: 912 70 394 303 668 +4: 399 658 944 993 991 +4: 923 166 541 409 64 +4: 769 42 125 676 744 +4: 70 794 301 506 793 +4: 469 9 393 597 307 +4: 223 73 718 222 745 +4: 954 763 442 579 943 +4: 527 596 114 253 25 +4: 315 560 873 611 370 +4: 171 112 886 10 900 +4: 704 409 771 596 496 +4: 756 851 877 813 847 +4: 556 564 554 295 333 +4: 828 592 22 129 222 +4: 452 436 557 587 967 +4: 652 167 973 764 373 +4: 349 144 571 122 61 +4: 272 75 823 929 545 +4: 173 568 756 335 42 +4: 86 275 73 413 882 +4: 523 423 791 368 752 +4: 667 768 754 642 140 +4: 646 634 408 340 777 +4: 461 304 505 346 555 +4: 517 950 371 474 379 +4: 889 843 640 941 223 +4: 680 988 88 22 71 +4: 114 650 409 185 991 +4: 204 122 218 906 419 +4: 781 761 300 71 846 +4: 576 9 550 334 726 +4: 193 243 692 281 13 +4: 179 696 354 949 625 +4: 503 870 716 956 677 +4: 746 698 625 722 490 +4: 768 743 412 600 523 +4: 277 772 100 876 799 +4: 529 692 61 431 220 +4: 141 458 552 190 238 +4: 701 921 558 888 277 +4: 44 384 70 228 425 +4: 991 202 224 386 163 +4: 507 775 544 622 356 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK @@ -2608,15 +2644,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -6: [2025-10-08 06:37:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -6: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:37:31] : LOG : Building guide tree. -6: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:37:31] : LOG : Aligning -6: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +6: [2026-11-10 13:04:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +6: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:04:54] : LOG : Building guide tree. +6: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:04:54] : LOG : Aligning +6: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2645,15 +2681,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -7: [2025-10-08 06:37:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -7: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:37:31] : LOG : Building guide tree. -7: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:37:31] : LOG : Aligning -7: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +7: [2026-11-10 13:04:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +7: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:04:54] : LOG : Building guide tree. +7: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:04:54] : LOG : Aligning +7: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2682,15 +2718,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -8: [2025-10-08 06:37:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -8: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:37:31] : LOG : Building guide tree. -8: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:37:31] : LOG : Aligning -8: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +8: [2026-11-10 13:04:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +8: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:04:54] : LOG : Building guide tree. +8: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:04:54] : LOG : Aligning +8: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2731,15 +2767,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -9: [2025-10-08 06:37:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -9: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:37:31] : LOG : Building guide tree. -9: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:37:31] : LOG : Aligning -9: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +9: [2026-11-10 13:04:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +9: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:04:54] : LOG : Building guide tree. +9: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:04:54] : LOG : Aligning +9: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2780,15 +2816,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -10: [2025-10-08 06:37:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -10: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:37:31] : LOG : Building guide tree. -10: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:37:31] : LOG : Aligning -10: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +10: [2026-11-10 13:04:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +10: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:04:54] : LOG : Building guide tree. +10: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:04:54] : LOG : Aligning +10: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -2815,13 +2851,15 @@ 10: Q---- 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 0.01 sec - 4/12 Test #5: C++Lib ........................... Passed 0.01 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 0.01 sec 6/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec 7/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec +12: [2026-11-10 13:04:54] : LOG : DSSim - a simplistic sequence simulator. +12: [2026-11-10 13:04:54] : LOG : Protein alignments - 20 seq 11: 11: Kalign (3.4.0) 11: @@ -2838,17 +2876,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-10-08 06:37:31] : LOG : Detected protein sequences. -11: [2025-10-08 06:37:31] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-10-08 06:37:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-10-08 06:37:31] : LOG : Calculating pairwise distances -12: [2025-10-08 06:37:31] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-10-08 06:37:31] : LOG : Protein alignments - 20 seq -11: [2025-10-08 06:37:31] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2025-10-08 06:37:31] : LOG : Building guide tree. -11: [2025-10-08 06:37:31] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-10-08 06:37:31] : LOG : Aligning -11: [2025-10-08 06:37:31] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2026-11-10 13:04:54] : LOG : Detected protein sequences. +11: [2026-11-10 13:04:54] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2026-11-10 13:04:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2026-11-10 13:04:54] : LOG : Calculating pairwise distances +11: [2026-11-10 13:04:54] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:04:54] : LOG : Building guide tree. +11: [2026-11-10 13:04:54] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:04:54] : LOG : Aligning +11: [2026-11-10 13:04:54] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -3157,41 +3193,41 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec +10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.06 sec 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2025-10-08 06:37:31] : LOG : Testing correctness of AVX bpm. +1: [2026-11-10 13:04:54] : LOG : Testing correctness of AVX bpm. 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% 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: LOG : 0.085040 - bpm_block -11/12 Test #1: bpm_utest ........................ Passed 5.94 sec +1: [2026-11-10 13:04:58] : LOG : Timing DYN 256 +1: [2026-11-10 13:05:00] : LOG : 1.353622 - dyn +1: [2026-11-10 13:05:00] : LOG : 0.000000 - bpm +1: [2026-11-10 13:05:00] : LOG : 0.084581 - bpm_block2 +1: [2026-11-10 13:05:00] : LOG : 0.084841 - bpm_block +11/12 Test #1: bpm_utest ........................ Passed 5.77 sec 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:37:45] : LOG : Protein alignments - 10000 seq +12: [2026-11-10 13:05:08] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-10-08 06:37:54] : LOG : DNA alignments - 20 seq +12: [2026-11-10 13:05:17] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 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[==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:37:57] : LOG : DNA alignments - 1000 seq +12: [2026-11-10 13:05:21] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:38:03] : LOG : DNA alignments - 10000 seq +12: [2026-11-10 13:05:26] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.06 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.22 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 36.07 sec +Total Test time (real) = 36.24 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_test make[1]: Entering directory '/build/reproducible-path/kalign-3.4.0' @@ -3220,24 +3256,24 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-10-08 06:38:07] : LOG : Testing correctness of serial bpm. +1: [2026-11-10 13:05:31] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2025-10-08 06:38:08] : LOG : Testing correctness of AVX bpm. +1: [2026-11-10 13:05:31] : LOG : Testing correctness of AVX bpm. 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: [2025-10-08 06:38:12] : LOG : Timing DYN 256 -1: [2025-10-08 06:38:13] : LOG : 1.354228 - dyn -1: [2025-10-08 06:38:13] : LOG : 0.055746 - bpm -1: [2025-10-08 06:38:13] : LOG : 0.082885 - bpm_block2 -1: [2025-10-08 06:38:13] : LOG : 0.083516 - bpm_block +1: [2026-11-10 13:05:35] : LOG : Timing DYN 256 +1: [2026-11-10 13:05:37] : LOG : 1.354275 - dyn +1: [2026-11-10 13:05:37] : LOG : 0.055659 - bpm +1: [2026-11-10 13:05:37] : LOG : 0.082532 - bpm_block2 +1: [2026-11-10 13:05:37] : LOG : 0.084816 - bpm_block 1/12 Test #1: bpm_utest ........................ Passed 5.96 sec test 2 Start 2: alphabet_utest @@ -3384,11 +3420,11 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 3: Test timeout computed to be: 1500 -3: [2025-10-08 06:38:13] : LOG : Check for correctness. -3: [2025-10-08 06:38:13] : LOG : Timing serial -3: [2025-10-08 06:38:13] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -3: [2025-10-08 06:38:13] : LOG : Timing AVX -3: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2026-11-10 13:05:37] : LOG : Check for correctness. +3: [2026-11-10 13:05:37] : LOG : Timing serial +3: [2026-11-10 13:05:37] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2026-11-10 13:05:37] : LOG : Timing AVX +3: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -3396,60 +3432,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib 4: Test timeout computed to be: 1500 -4: 419 406 796 807 630 -4: 108 765 999 826 526 -4: 870 315 981 117 668 -4: 35 809 528 153 236 -4: 777 783 122 906 617 -4: 498 269 273 30 369 -4: 102 899 365 985 147 -4: 469 505 922 978 14 -4: 743 305 692 447 546 -4: 768 459 674 757 576 -4: 684 548 451 530 253 -4: 230 183 314 889 623 -4: 992 686 377 83 855 -4: 964 790 318 427 905 -4: 481 519 139 314 748 -4: 799 55 622 318 287 -4: 296 566 836 237 505 -4: 954 716 168 744 997 -4: 211 221 500 687 817 -4: 668 623 366 963 419 -4: 927 348 178 508 266 -4: 174 397 709 637 845 -4: 864 205 893 200 830 -4: 551 816 669 780 21 -4: 861 881 268 789 104 -4: 852 933 510 287 578 -4: 294 171 351 111 510 -4: 744 557 437 704 928 -4: 34 679 759 484 431 -4: 830 869 475 751 434 -4: 642 660 139 153 709 -4: 885 910 323 287 147 -4: 863 776 269 307 509 -4: 275 61 319 324 399 -4: 289 254 474 794 459 -4: 225 959 882 691 207 -4: 47 26 109 973 783 -4: 453 94 80 305 881 -4: 374 213 979 41 576 -4: 95 809 541 229 845 -4: 730 842 389 596 949 -4: 28 71 428 533 237 -4: 576 994 567 999 852 -4: 950 220 419 812 398 -4: 62 386 114 37 651 -4: 421 114 653 269 863 -4: 922 259 644 317 396 -4: 792 797 306 87 929 -4: 914 838 881 581 356 -4: 145 436 230 877 39 -4: 975 940 505 919 502 -4: 168 149 932 69 463 -4: 206 974 255 811 50 -4: 880 107 840 11 204 +4: 208 809 106 809 776 +4: 459 197 465 702 338 +4: 648 293 155 787 859 +4: 166 153 265 832 555 +4: 280 886 265 262 679 +4: 154 809 976 914 900 +4: 773 228 278 367 166 +4: 401 236 34 350 64 +4: 378 958 964 554 820 +4: 79 128 430 563 312 +4: 573 239 146 792 892 +4: 559 771 345 527 623 +4: 400 260 113 218 14 +4: 378 810 204 909 671 +4: 397 518 223 757 352 +4: 839 836 809 977 364 +4: 243 854 938 127 852 +4: 459 932 933 131 159 +4: 482 439 649 911 510 +4: 862 496 634 428 311 +4: 884 68 373 145 683 +4: 612 30 65 473 797 +4: 744 253 392 88 331 +4: 924 284 770 278 89 +4: 607 552 316 626 667 +4: 175 936 367 473 78 +4: 891 921 978 571 104 +4: 999 761 811 948 632 +4: 618 432 552 421 29 +4: 555 777 186 225 460 +4: 122 378 619 154 287 +4: 779 620 901 763 617 +4: 320 482 87 686 933 +4: 704 355 559 74 594 +4: 339 406 489 359 266 +4: 364 479 369 226 756 +4: 313 755 879 885 83 +4: 71 651 325 117 813 +4: 718 200 510 192 797 +4: 858 84 574 497 645 +4: 763 859 352 130 351 +4: 967 630 545 255 953 +4: 797 162 184 144 765 +4: 993 571 700 745 203 +4: 207 560 778 733 882 +4: 546 271 967 943 315 +4: 921 678 109 839 47 +4: 594 627 498 185 91 +4: 341 743 542 548 974 +4: 881 276 732 535 556 +4: 874 335 771 431 681 +4: 332 260 707 353 453 +4: 167 24 625 514 234 +4: 622 219 655 163 30 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -3485,15 +3521,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-10-08 06:38:13] : LOG : Detected protein sequences. -6: [2025-10-08 06:38:13] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:13] : LOG : Calculating pairwise distances -6: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:13] : LOG : Building guide tree. -6: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:13] : LOG : Aligning -6: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +6: [2026-11-10 13:05:37] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +6: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:05:37] : LOG : Building guide tree. +6: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:05:37] : LOG : Aligning +6: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3529,15 +3565,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-10-08 06:38:13] : LOG : Detected protein sequences. -7: [2025-10-08 06:38:13] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:13] : LOG : Calculating pairwise distances -7: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:13] : LOG : Building guide tree. -7: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:13] : LOG : Aligning -7: [2025-10-08 06:38:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +7: [2026-11-10 13:05:37] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +7: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:05:37] : LOG : Building guide tree. +7: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:05:37] : LOG : Aligning +7: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3573,15 +3609,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-10-08 06:38:14] : LOG : Detected protein sequences. -8: [2025-10-08 06:38:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:01.00 -8: [2025-10-08 06:38:14] : LOG : Calculating pairwise distances -8: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:38:14] : LOG : Building guide tree. -8: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:38:14] : LOG : Aligning -8: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +8: [2026-11-10 13:05:37] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +8: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:05:37] : LOG : Building guide tree. +8: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:05:37] : LOG : Aligning +8: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3629,15 +3665,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-10-08 06:38:14] : LOG : Detected protein sequences. -9: [2025-10-08 06:38:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:14] : LOG : Calculating pairwise distances -9: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:14] : LOG : Building guide tree. -9: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:14] : LOG : Aligning -9: [2025-10-08 06:38:14] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +9: [2026-11-10 13:05:37] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +9: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:05:37] : LOG : Building guide tree. +9: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:05:37] : LOG : Aligning +9: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3685,15 +3721,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-10-08 06:38:14] : LOG : Detected protein sequences. -10: [2025-10-08 06:38:14] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:14] : LOG : Calculating pairwise distances -10: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:14] : LOG : Building guide tree. -10: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:14] : LOG : Aligning -10: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +10: [2026-11-10 13:05:37] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +10: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:05:37] : LOG : Building guide tree. +10: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:05:37] : LOG : Aligning +10: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3741,15 +3777,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-10-08 06:38:14] : LOG : Detected protein sequences. -11: [2025-10-08 06:38:14] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-10-08 06:38:14] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:14] : LOG : Calculating pairwise distances -11: [2025-10-08 06:38:14] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:14] : LOG : Building guide tree. -11: [2025-10-08 06:38:14] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:14] : LOG : Aligning -11: [2025-10-08 06:38:14] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2026-11-10 13:05:37] : LOG : Detected protein sequences. +11: [2026-11-10 13:05:37] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2026-11-10 13:05:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2026-11-10 13:05:37] : LOG : Calculating pairwise distances +11: [2026-11-10 13:05:37] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +11: [2026-11-10 13:05:37] : LOG : Building guide tree. +11: [2026-11-10 13:05:37] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:05:37] : LOG : Aligning +11: [2026-11-10 13:05:37] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -4065,24 +4101,24 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2025-10-08 06:38:14] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-10-08 06:38:14] : LOG : Protein alignments - 20 seq +12: [2026-11-10 13:05:37] : LOG : DSSim - a simplistic sequence simulator. +12: [2026-11-10 13:05:37] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 10% 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:38:17] : LOG : Protein alignments - 1000 seq +12: [2026-11-10 13:05:41] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:38:27] : LOG : Protein alignments - 10000 seq +12: [2026-11-10 13:05:51] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-10-08 06:38:36] : LOG : DNA alignments - 20 seq +12: [2026-11-10 13:05:59] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:38:39] : LOG : DNA alignments - 1000 seq +12: [2026-11-10 13:06:03] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:38:44] : LOG : DNA alignments - 10000 seq +12: [2026-11-10 13:06:08] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 34.24 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 34.26 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 40.30 sec +Total Test time (real) = 40.59 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx/DartConfiguration.tcl @@ -4101,25 +4137,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-10-08 06:38:48] : LOG : Testing correctness of serial bpm. +1: [2026-11-10 13:06:12] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2025-10-08 06:38:48] : LOG : Testing correctness of AVX bpm. +1: [2026-11-10 13:06:12] : LOG : Testing correctness of AVX bpm. 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: [2025-10-08 06:38:52] : LOG : Timing DYN 256 -1: [2025-10-08 06:38:54] : LOG : 1.354135 - dyn -1: [2025-10-08 06:38:54] : LOG : 0.000000 - bpm -1: [2025-10-08 06:38:54] : LOG : 0.085115 - bpm_block2 -1: [2025-10-08 06:38:54] : LOG : 0.085240 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 5.78 sec +1: [2026-11-10 13:06:16] : LOG : Timing DYN 256 +1: [2026-11-10 13:06:17] : LOG : 1.354134 - dyn +1: [2026-11-10 13:06:17] : LOG : 0.000000 - bpm +1: [2026-11-10 13:06:17] : LOG : 0.084945 - bpm_block2 +1: [2026-11-10 13:06:17] : LOG : 0.084911 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 5.80 sec test 2 Start 2: alphabet_utest @@ -4265,9 +4301,9 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 3: Test timeout computed to be: 1500 -3: [2025-10-08 06:38:54] : LOG : Check for correctness. -3: [2025-10-08 06:38:54] : LOG : Timing serial -3: [2025-10-08 06:38:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2026-11-10 13:06:17] : LOG : Check for correctness. +3: [2026-11-10 13:06:17] : LOG : Timing serial +3: [2026-11-10 13:06:17] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -4275,60 +4311,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 4: Test timeout computed to be: 1500 -4: 517 347 474 270 282 -4: 721 669 190 417 874 -4: 175 953 106 768 694 -4: 114 723 542 336 27 -4: 917 360 281 211 675 -4: 871 948 686 477 788 -4: 118 391 963 329 725 -4: 529 441 136 856 538 -4: 361 14 194 638 324 -4: 536 623 955 42 247 -4: 149 575 510 454 643 -4: 173 783 206 257 589 -4: 717 566 28 361 622 -4: 784 377 442 338 249 -4: 726 372 153 414 20 -4: 634 881 74 417 711 -4: 612 706 840 315 160 -4: 348 21 661 376 666 -4: 696 64 625 628 918 -4: 213 304 22 491 778 -4: 786 316 509 811 69 -4: 511 980 901 556 471 -4: 0 275 597 427 12 -4: 821 525 525 482 333 -4: 688 992 152 399 426 -4: 738 597 690 431 106 -4: 829 378 130 616 38 -4: 755 673 823 292 744 -4: 763 838 905 56 787 -4: 8 804 970 777 644 -4: 540 727 440 135 347 -4: 897 36 61 932 636 -4: 57 159 184 718 756 -4: 599 143 72 683 788 -4: 520 787 738 610 354 -4: 326 120 751 425 974 -4: 739 543 971 612 917 -4: 107 511 741 105 811 -4: 201 298 933 15 860 -4: 933 983 392 625 240 -4: 596 889 619 570 247 -4: 776 296 580 580 637 -4: 702 955 275 92 299 -4: 236 980 583 259 22 -4: 492 632 929 555 139 -4: 102 986 607 592 640 -4: 699 14 350 913 18 -4: 573 107 782 780 939 -4: 103 444 68 39 505 -4: 345 8 949 365 102 -4: 654 940 798 513 440 -4: 462 59 431 218 179 -4: 987 632 381 493 808 -4: 351 656 182 793 412 +4: 669 803 536 845 3 +4: 675 353 650 46 647 +4: 226 300 215 119 153 +4: 81 507 561 568 807 +4: 498 81 586 261 184 +4: 70 235 770 386 506 +4: 269 857 861 359 189 +4: 20 977 770 203 181 +4: 773 494 883 367 907 +4: 976 738 627 792 374 +4: 616 359 826 968 246 +4: 794 643 173 792 701 +4: 542 575 449 561 574 +4: 922 604 322 302 397 +4: 841 900 7 596 176 +4: 914 590 556 379 877 +4: 819 368 652 730 789 +4: 238 551 742 688 953 +4: 100 361 704 143 562 +4: 757 320 201 586 832 +4: 999 3 252 68 321 +4: 438 461 878 949 894 +4: 48 153 32 158 933 +4: 667 929 555 667 695 +4: 841 710 712 942 778 +4: 977 630 969 114 732 +4: 8 777 122 783 351 +4: 202 790 964 645 184 +4: 753 502 517 282 69 +4: 107 660 439 312 738 +4: 829 505 130 699 645 +4: 576 371 380 860 760 +4: 618 484 288 67 880 +4: 118 462 530 63 919 +4: 33 570 784 429 707 +4: 180 49 234 735 357 +4: 113 696 306 810 216 +4: 586 848 104 143 321 +4: 47 727 178 850 38 +4: 850 570 222 625 828 +4: 965 47 406 410 532 +4: 705 887 760 6 65 +4: 456 944 514 313 839 +4: 223 594 770 641 538 +4: 161 369 680 370 726 +4: 530 590 887 998 303 +4: 94 742 330 990 486 +4: 125 850 615 114 798 +4: 352 442 88 223 461 +4: 252 673 24 869 458 +4: 876 828 158 463 297 +4: 779 199 265 169 926 +4: 542 824 540 712 780 +4: 622 461 421 638 915 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -4364,15 +4400,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -6: [2025-10-08 06:38:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -6: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:54] : LOG : Building guide tree. -6: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:38:54] : LOG : Aligning -6: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:06:17] : LOG : Detected protein sequences. +6: [2026-11-10 13:06:17] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:06:17] : LOG : Calculating pairwise distances +6: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:06:17] : LOG : Building guide tree. +6: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:06:17] : LOG : Aligning +6: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4408,15 +4444,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -7: [2025-10-08 06:38:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -7: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:54] : LOG : Building guide tree. -7: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:38:54] : LOG : Aligning -7: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:06:17] : LOG : Detected protein sequences. +7: [2026-11-10 13:06:17] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:06:17] : LOG : Calculating pairwise distances +7: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:06:17] : LOG : Building guide tree. +7: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:06:17] : LOG : Aligning +7: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4452,15 +4488,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -8: [2025-10-08 06:38:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -8: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:38:54] : LOG : Building guide tree. -8: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:38:54] : LOG : Aligning -8: [2025-10-08 06:38:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:06:17] : LOG : Detected protein sequences. +8: [2026-11-10 13:06:17] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2026-11-10 13:06:17] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:06:17] : LOG : Calculating pairwise distances +8: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:01.00 +8: [2026-11-10 13:06:18] : LOG : Building guide tree. +8: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:06:18] : LOG : Aligning +8: [2026-11-10 13:06:18] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4508,15 +4544,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -9: [2025-10-08 06:38:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -9: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:54] : LOG : Building guide tree. -9: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:38:54] : LOG : Aligning -9: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:06:18] : LOG : Detected protein sequences. +9: [2026-11-10 13:06:18] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:06:18] : LOG : Calculating pairwise distances +9: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:06:18] : LOG : Building guide tree. +9: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:06:18] : LOG : Aligning +9: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4564,15 +4600,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -10: [2025-10-08 06:38:54] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -10: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:54] : LOG : Building guide tree. -10: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:38:54] : LOG : Aligning -10: [2025-10-08 06:38:54] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:06:18] : LOG : Detected protein sequences. +10: [2026-11-10 13:06:18] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:06:18] : LOG : Calculating pairwise distances +10: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:06:18] : LOG : Building guide tree. +10: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:06:18] : LOG : Aligning +10: [2026-11-10 13:06:18] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4620,15 +4656,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-10-08 06:38:54] : LOG : Detected protein sequences. -11: [2025-10-08 06:38:54] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-10-08 06:38:54] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:54] : LOG : Calculating pairwise distances -11: [2025-10-08 06:38:54] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:54] : LOG : Building guide tree. -11: [2025-10-08 06:38:54] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -11: [2025-10-08 06:38:54] : LOG : Aligning -11: [2025-10-08 06:38:54] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2026-11-10 13:06:18] : LOG : Detected protein sequences. +11: [2026-11-10 13:06:18] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2026-11-10 13:06:18] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2026-11-10 13:06:18] : LOG : Calculating pairwise distances +11: [2026-11-10 13:06:18] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2026-11-10 13:06:18] : LOG : Building guide tree. +11: [2026-11-10 13:06:18] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2026-11-10 13:06:18] : LOG : Aligning +11: [2026-11-10 13:06:18] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -4944,24 +4980,24 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2025-10-08 06:38:54] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-10-08 06:38:54] : LOG : Protein alignments - 20 seq +12: [2026-11-10 13:06:18] : LOG : DSSim - a simplistic sequence simulator. +12: [2026-11-10 13:06:18] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 10% 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:38:57] : LOG : Protein alignments - 1000 seq +12: [2026-11-10 13:06:21] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:39:08] : LOG : Protein alignments - 10000 seq +12: [2026-11-10 13:06:32] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-10-08 06:39:18] : LOG : DNA alignments - 20 seq +12: [2026-11-10 13:06:41] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:39:21] : LOG : DNA alignments - 1000 seq +12: [2026-11-10 13:06:45] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:39:26] : LOG : DNA alignments - 10000 seq +12: [2026-11-10 13:06:50] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.61 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.46 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 42.49 sec +Total Test time (real) = 42.58 sec UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-sse4.1/DartConfiguration.tcl @@ -4980,25 +5016,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-10-08 06:39:30] : LOG : Testing correctness of serial bpm. +1: [2026-11-10 13:06:54] : LOG : Testing correctness of serial bpm. 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: 0 0 0 0 1: -1: [2025-10-08 06:39:30] : LOG : Testing correctness of AVX bpm. +1: [2026-11-10 13:06:54] : LOG : Testing correctness of AVX bpm. 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: [2025-10-08 06:39:35] : LOG : Timing DYN 256 -1: [2025-10-08 06:39:36] : LOG : 1.357636 - dyn -1: [2025-10-08 06:39:36] : LOG : 0.000000 - bpm -1: [2025-10-08 06:39:36] : LOG : 0.084772 - bpm_block2 -1: [2025-10-08 06:39:36] : LOG : 0.084926 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 5.80 sec +1: [2026-11-10 13:06:59] : LOG : Timing DYN 256 +1: [2026-11-10 13:07:00] : LOG : 1.354088 - dyn +1: [2026-11-10 13:07:00] : LOG : 0.000000 - bpm +1: [2026-11-10 13:07:00] : LOG : 0.084692 - bpm_block2 +1: [2026-11-10 13:07:00] : LOG : 0.085565 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 5.78 sec test 2 Start 2: alphabet_utest @@ -5144,9 +5180,9 @@ 3: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/edist_utest 3: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 3: Test timeout computed to be: 1500 -3: [2025-10-08 06:39:36] : LOG : Check for correctness. -3: [2025-10-08 06:39:36] : LOG : Timing serial -3: [2025-10-08 06:39:36] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +3: [2026-11-10 13:07:00] : LOG : Check for correctness. +3: [2026-11-10 13:07:00] : LOG : Timing serial +3: [2026-11-10 13:07:00] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 3/12 Test #3: edist_utest ...................... Passed 0.01 sec test 4 Start 4: task_utest @@ -5154,60 +5190,60 @@ 4: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib/task_utest 4: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/lib 4: Test timeout computed to be: 1500 -4: 264 633 213 102 127 -4: 755 447 302 14 764 -4: 496 199 800 777 577 -4: 960 314 378 99 366 -4: 340 608 341 780 843 -4: 893 373 591 49 589 -4: 27 599 976 72 516 -4: 224 739 648 258 419 -4: 309 847 712 149 262 -4: 14 160 339 914 863 -4: 903 942 106 239 402 -4: 123 44 475 658 793 -4: 805 593 656 431 781 -4: 204 981 415 788 88 -4: 988 481 923 513 369 -4: 661 470 92 971 893 -4: 422 542 281 361 812 -4: 570 948 42 457 184 -4: 747 638 743 430 854 -4: 255 988 715 884 77 -4: 768 70 62 55 203 -4: 253 558 577 574 295 -4: 904 471 330 22 767 -4: 603 201 337 873 999 -4: 857 20 134 302 533 -4: 543 687 391 285 898 -4: 406 17 132 657 217 -4: 811 83 773 427 659 -4: 719 652 590 684 661 -4: 450 8 992 244 226 -4: 896 443 643 872 404 -4: 662 356 786 926 674 -4: 698 816 825 436 331 -4: 535 133 938 796 149 -4: 98 901 937 578 733 -4: 36 119 460 970 481 -4: 98 479 289 12 53 -4: 635 655 310 983 432 -4: 131 903 452 467 326 -4: 328 78 162 425 325 -4: 379 469 463 44 296 -4: 639 903 222 111 184 -4: 506 768 138 414 143 -4: 9 681 717 726 413 -4: 934 126 452 319 506 -4: 136 237 25 888 243 -4: 148 162 710 100 836 -4: 275 572 132 928 474 -4: 4 739 625 15 660 -4: 776 478 458 977 203 -4: 121 405 494 136 710 -4: 910 146 38 528 31 -4: 66 804 608 842 709 -4: 317 319 897 463 159 +4: 966 805 676 853 78 +4: 809 797 551 489 943 +4: 592 937 288 662 253 +4: 394 932 986 720 636 +4: 831 711 495 676 246 +4: 67 815 69 265 184 +4: 308 80 416 455 485 +4: 187 150 99 477 966 +4: 79 862 68 726 288 +4: 601 992 106 826 391 +4: 459 587 64 406 140 +4: 375 98 789 830 376 +4: 991 194 543 416 504 +4: 885 525 653 499 922 +4: 947 800 431 307 925 +4: 547 857 357 472 528 +4: 476 897 471 240 633 +4: 874 783 841 266 971 +4: 291 41 538 644 997 +4: 605 820 113 798 744 +4: 42 436 1 129 670 +4: 841 374 3 206 726 +4: 642 521 731 951 814 +4: 987 182 451 147 511 +4: 390 646 239 960 792 +4: 871 925 98 765 452 +4: 550 754 35 542 238 +4: 426 427 597 289 380 +4: 981 389 328 401 60 +4: 634 804 134 593 895 +4: 513 358 561 464 84 +4: 744 481 154 470 18 +4: 916 921 157 158 596 +4: 42 724 609 87 827 +4: 540 429 689 736 350 +4: 810 875 477 378 425 +4: 888 337 675 692 445 +4: 969 245 501 256 814 +4: 378 116 183 408 677 +4: 901 449 657 695 1 +4: 737 833 470 964 909 +4: 316 702 817 702 402 +4: 740 823 917 661 205 +4: 839 927 430 232 646 +4: 664 174 425 837 982 +4: 65 694 405 203 821 +4: 121 505 596 332 40 +4: 278 672 844 150 362 +4: 986 773 439 855 114 +4: 203 295 216 57 542 +4: 579 834 764 322 691 +4: 453 11 619 249 687 +4: 785 790 667 658 172 +4: 211 376 967 620 279 4/12 Test #4: task_utest ....................... Passed 0.00 sec test 5 Start 5: C++Lib @@ -5243,15 +5279,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -6: [2025-10-08 06:39:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -6: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:39:36] : LOG : Building guide tree. -6: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-10-08 06:39:36] : LOG : Aligning -6: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +6: [2026-11-10 13:07:00] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +6: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:07:00] : LOG : Building guide tree. +6: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2026-11-10 13:07:00] : LOG : Aligning +6: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -5264,7 +5300,7 @@ 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.00 sec + 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.02 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf @@ -5287,15 +5323,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -7: [2025-10-08 06:39:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -7: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:39:36] : LOG : Building guide tree. -7: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-10-08 06:39:36] : LOG : Aligning -7: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +7: [2026-11-10 13:07:00] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +7: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:07:00] : LOG : Building guide tree. +7: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2026-11-10 13:07:00] : LOG : Aligning +7: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -5308,7 +5344,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.00 sec + 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.03 sec test 8 Start 8: kalign_itest_BB12006.msf @@ -5331,15 +5367,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -8: [2025-10-08 06:39:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -8: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:39:36] : LOG : Building guide tree. -8: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-10-08 06:39:36] : LOG : Aligning -8: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +8: [2026-11-10 13:07:00] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +8: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:07:00] : LOG : Building guide tree. +8: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2026-11-10 13:07:00] : LOG : Aligning +8: [2026-11-10 13:07:00] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5387,15 +5423,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -9: [2025-10-08 06:39:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -9: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:39:36] : LOG : Building guide tree. -9: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-10-08 06:39:36] : LOG : Aligning -9: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +9: [2026-11-10 13:07:00] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +9: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:07:00] : LOG : Building guide tree. +9: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2026-11-10 13:07:00] : LOG : Aligning +9: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5443,15 +5479,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -10: [2025-10-08 06:39:36] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -10: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:39:36] : LOG : Building guide tree. -10: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-10-08 06:39:36] : LOG : Aligning -10: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +10: [2026-11-10 13:07:00] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +10: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:07:00] : LOG : Building guide tree. +10: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2026-11-10 13:07:00] : LOG : Aligning +10: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5499,15 +5535,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-10-08 06:39:36] : LOG : Detected protein sequences. -11: [2025-10-08 06:39:36] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-10-08 06:39:36] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-10-08 06:39:36] : LOG : Calculating pairwise distances -11: [2025-10-08 06:39:36] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2025-10-08 06:39:36] : LOG : Building guide tree. -11: [2025-10-08 06:39:36] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-10-08 06:39:36] : LOG : Aligning -11: [2025-10-08 06:39:36] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:07:00] : LOG : Detected protein sequences. +11: [2026-11-10 13:07:00] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2026-11-10 13:07:00] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2026-11-10 13:07:00] : LOG : Calculating pairwise distances +11: [2026-11-10 13:07:00] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:07:00] : LOG : Building guide tree. +11: [2026-11-10 13:07:00] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +11: [2026-11-10 13:07:00] : LOG : Aligning +11: [2026-11-10 13:07:00] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -5823,29 +5859,29 @@ 12: Test command: /build/reproducible-path/kalign-3.4.0/obj-sse4.1/tests/dssim 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 -12: [2025-10-08 06:39:37] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-10-08 06:39:37] : LOG : Protein alignments - 20 seq +12: [2026-11-10 13:07:00] : LOG : DSSim - a simplistic sequence simulator. +12: [2026-11-10 13:07:00] : LOG : Protein alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [==== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 9% [===== ] 10% [===== ] 10% [===== ] 10% [===== ] 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[==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-10-08 06:39:40] : LOG : Protein alignments - 1000 seq +12: [2026-11-10 13:07:04] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-10-08 06:39:51] : LOG : Protein alignments - 10000 seq +12: [2026-11-10 13:07:15] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-10-08 06:40:00] : LOG : DNA alignments - 20 seq +12: [2026-11-10 13:07:24] : LOG : DNA alignments - 20 seq 12: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [ ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 1% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 2% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [= ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 3% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 4% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 5% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 6% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [=== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 7% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 8% 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] 90% [==================================================] 100% -12: [2025-10-08 06:40:09] : LOG : DNA alignments - 10000 seq +12: [2026-11-10 13:07:33] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.41 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 36.66 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 42.58 sec +Total Test time (real) = 42.73 sec make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kalign/ - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/kalign-3.4.0/debian/kalign AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/kalign-3.4.0 -B/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5913,12 +5949,14 @@ 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/2014747/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2014747/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/1362583 and its subdirectories -I: Current time: Tue Oct 7 18:40:30 -12 2025 -I: pbuilder-time-stamp: 1759905630 +I: removing directory /srv/workspace/pbuilder/2014747 and its subdirectories +I: Current time: Wed Nov 11 03:07:58 +14 2026 +I: pbuilder-time-stamp: 1794316078