Diff of the two buildlogs: -- --- b1/build.log 2024-06-01 09:09:14.820749824 +0000 +++ b2/build.log 2024-06-01 09:28:28.675666999 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 4 03:13:20 -12 2025 -I: pbuilder-time-stamp: 1751642000 +I: Current time: Sat Jun 1 23:09:18 +14 2024 +I: pbuilder-time-stamp: 1717232958 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ 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/119659/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3073256/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Jun 1 09:09 /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/3073256/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3073256/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=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4def963ed1ee4c7fb181adfd5c16ee5b' - 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='119659' - PS1='# ' - PS2='> ' + INVOCATION_ID=f0a75eeabab64c628fe583e50542f27b + 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=3073256 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.2Lv4qtnt/pbuilderrc_5mCM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2Lv4qtnt/b1 --logfile b1/build.log kalign_3.4.0-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2Lv4qtnt/pbuilderrc_NQaJ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2Lv4qtnt/b2 --logfile b2/build.log kalign_3.4.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/119659/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 1 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3073256/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -164,7 +196,7 @@ Get: 52 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] -Fetched 36.2 MB in 1s (41.4 MB/s) +Fetched 36.2 MB in 9s (3864 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19719 files and directories currently installed.) @@ -395,7 +427,11 @@ 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/3073256/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3073256/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 @@ -446,7 +482,7 @@ -- 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 (17.6s) +-- Configuring done (8.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -496,8 +532,8 @@ -- 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 (27.9s) --- Generating done (0.1s) +-- Configuring done (8.4s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -549,8 +585,8 @@ -- 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 (7.7s) --- Generating done (0.2s) +-- Configuring done (12.6s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -605,8 +641,8 @@ -- 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 (22.7s) --- Generating done (0.1s) +-- Configuring done (13.2s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -619,69 +655,116 @@ -- 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 -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "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 make -f CMakeFiles/Makefile2 all make[2]: Entering 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/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_OBJ.dir/DependInfo.cmake "--color=" make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend -make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend 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/tldevel.dir/DependInfo.cmake "--color=" -make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend -make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-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_OBJ.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/bpm_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.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/alphabet_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-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/edist_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-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/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 -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build +make[3]: Entering 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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make[3]: Leaving 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 -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/build -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[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_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]: 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' +[ 1%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +make[3]: Leaving 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 -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build +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 make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o -[ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 4%] Building C object lib/CMakeFiles/task_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 -g -O2 -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 -[ 5%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -[ 6%] 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/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 -[ 8%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.c.o +[ 2%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.c.o +[ 4%] 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/lib/src -g -O2 -Werror=implicit-function-declaration 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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/tlrng.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c +cd /build/reproducible-path/kalign-3.4.0/obj-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 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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 +[ 21%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +[ 22%] 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 -g -O2 -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/kalign_OBJ.dir/src/msa_alloc.c.o -[ 14%] 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 -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_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 +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/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-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 +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 +[ 25%] Building C object lib/CMakeFiles/task_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 -g -O2 -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 +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +[ 27%] 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 -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 -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/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 +[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.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_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 +[ 29%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.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/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 +[ 31%] 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 -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 +[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.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_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 +[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.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 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CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_cmp.c +[ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o +[ 37%] 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/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 +[ 39%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +[ 40%] 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 -g -O2 -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 +[ 41%] 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 -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/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 +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 +[ 43%] 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/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 -[ 16%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +[ 45%] Building C object lib/CMakeFiles/task_utest.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/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 -g -O2 -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 -[ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o /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; @@ -693,248 +776,194 @@ /build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building C object lib/CMakeFiles/bpm_utest.dir/src/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=. -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 -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 /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/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 -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_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 -cd 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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 -[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -[ 35%] 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/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 +/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP 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/build/reproducible-path/kalign-3.4.0/lib/src/aln_param.c +[ 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 +[ 56%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o cd 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-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-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_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 +[ 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 -[ 47%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o -[ 48%] Building C object lib/CMakeFiles/bpm_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/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-x86_64-linux-gnu/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration 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/build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c -[ 60%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.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_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 -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -cd 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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/weave_alignment.c.o -MF CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c +[ 66%] Linking C executable 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 /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 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 -[ 64%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.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/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 make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 64%] Built target edist_utest -[ 66%] 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 -/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 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 -[ 67%] 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 -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 -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 67%] Built target task_utest -[ 68%] 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 -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' -[ 68%] Built target tldevel -[ 70%] 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 -/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 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 +[ 66%] Built target edist_utest make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 70%] Built target kalign_OBJ +[ 66%] Built target kalign_OBJ make -f lib/CMakeFiles/kalign.dir/build.make lib/CMakeFiles/kalign.dir/depend +[ 67%] Linking C static library libtldevel.a 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_static.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.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' +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 +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=" 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 +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 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_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' -[ 71%] Linking C static library libkalign.a -[ 70%] Built target bpm_utest +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o CMakeFiles/tldevel.dir/src/tlmisc.c.o CMakeFiles/tldevel.dir/src/tlrng.c.o CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o +[ 68%] 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.dir/cmake_clean_target.cmake -[ 72%] Linking C static library libkalign_static.a +[ 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 +[ 71%] Linking C static library libkalign_static.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 +/usr/bin/ranlib libtldevel.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 -fPIC -Wl,-z,relro -Wl,-z,now 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 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 +make[3]: Leaving 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/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 -[ 74%] 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 /usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o CMakeFiles/kalign_OBJ.dir/src/task.c.o CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o CMakeFiles/kalign_OBJ.dir/src/bpm.c.o CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o CMakeFiles/kalign_OBJ.dir/src/aln_controller.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -/usr/bin/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 CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +[ 71%] Built target tldevel +[ 72%] 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 /usr/bin/ranlib libkalign_static.a +[ 74%] 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 /usr/bin/ranlib libkalign.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 -fPIC -Wl,-z,relro -Wl,-z,now 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 +/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 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' 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' [ 74%] Built target kalign_static make -f src/CMakeFiles/kalign-bin.dir/build.make src/CMakeFiles/kalign-bin.dir/depend +[ 74%] Built target task_utest make -f tests/CMakeFiles/largebench.dir/build.make tests/CMakeFiles/largebench.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/kalign-bin.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 /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/largebench.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 74%] Built target alphabet_utest [ 74%] Built target kalign make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.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 -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 -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/depend -make[3]: Leaving 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' 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 -f tests/CMakeFiles/kalign_io_test.dir/build.make tests/CMakeFiles/kalign_io_test.dir/depend make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -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 /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu/tests/CMakeFiles/kalign_lib_test.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends 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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 +[ 86%] Building C object src/CMakeFiles/kalignfmt.dir/parameters.c.o +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 +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.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 tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/build +make[3]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 87%] Building C object tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o +[ 89%] Building CXX object tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o 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 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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 -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 -[ 87%] Building C object tests/CMakeFiles/dssim.dir/dssim.c.o -[ 89%] Building C object tests/CMakeFiles/dssim.dir/dssim_test.c.o -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 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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 [ 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 /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 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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -[ 91%] Linking C executable kalign_cmp_test +[ 91%] 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 +[ 93%] 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 +/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 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/13/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 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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 -Wl,-z,relro -Wl,-z,now CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/13/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' 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 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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -[ 93%] Built target kalign_cmp_test -[ 94%] Linking C executable kalign -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 -/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 "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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -[ 95%] Linking C executable kalignfmt make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 95%] 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"CMakeFiles/kalign-bin.dir/parameters.c.o" -o kalign ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/13/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' -[ 95%] Built target kalign-bin -make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' -[ 97%] Linking C executable largebench [ 97%] Built target kalignfmt -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 -/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 CMakeFiles/largebench.dir/large_benchmark.c.o -o largebench ../lib/libtldevel.a ../lib/libkalign_static.a -lm /usr/lib/gcc/x86_64-linux-gnu/13/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%] 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 -[ 98%] Built target largebench -/usr/bin/cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/kalign-3.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -Wl,-z,relro -Wl,-z,now 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/13/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 dssim /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", @@ -948,10 +977,17 @@ /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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' +[ 98%] 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 +[ 98%] 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 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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a [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 CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -o kaligncpp ../lib/libkalign.a -lm /usr/lib/gcc/x86_64-linux-gnu/13/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 +make[3]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-x86_64-linux-gnu' [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 @@ -959,7 +995,7 @@ 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 -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-sse4.1 && make -j20 "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 @@ -967,139 +1003,137 @@ make[3]: Entering 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/depend make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/depend -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/depend -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.dir/depend -make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend -make -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/tldevel.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_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/alphabet_utest.dir/DependInfo.cmake "--color=" +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/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[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' +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend +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/alphabet_utest.dir/DependInfo.cmake "--color=" +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/edist_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +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' 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]: 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 lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.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 +[ 1%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o +make[4]: Entering 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' +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/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 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 -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build -make -f lib/CMakeFiles/alphabet_utest.dir/build.make lib/CMakeFiles/alphabet_utest.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' +[ 2%] 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 -g -O2 -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 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 lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build -make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 8%] Building C object 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CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/esl_stopwatch.c +[ 6%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' +[ 6%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o +make -f lib/CMakeFiles/task_utest.dir/build.make lib/CMakeFiles/task_utest.dir/build +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/tldevel.c.o -MF CMakeFiles/alphabet_utest.dir/src/tldevel.c.o.d -o 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-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 -[ 18%] Building C object lib/CMakeFiles/task_utest.dir/src/tldevel.c.o -[ 20%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.c.o -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 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/build/reproducible-path/kalign-3.4.0/lib/src/tlmisc.c -[ 21%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o +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/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 +[ 9%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.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/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-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 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/build/reproducible-path/kalign-3.4.0/lib/src/msa_alloc.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_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_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 -[ 24%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o -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 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CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/msa_misc.c -[ 27%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +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 +[ 10%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o +[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +[ 13%] Building C object lib/CMakeFiles/tldevel.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/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-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 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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 +[ 16%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +[ 17%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o +[ 14%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o +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 -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 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lib/CMakeFiles/task_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/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 +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 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/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 -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 +[ 25%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_op.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 -g -O2 -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 +[ 27%] Building C object lib/CMakeFiles/tldevel.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/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_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 -[ 28%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o -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_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 -[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.c.o -[ 32%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -[ 32%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o -[ 33%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.c.o -[ 29%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/tldevel.c.o -[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.c.o -[ 36%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o -[ 37%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -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 -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 -[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o -[ 41%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -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 -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 -[ 35%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -[ 44%] 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/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/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-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 +[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.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 +[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.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 +[ 31%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.c.o 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 -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 -[ 44%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.c.o -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/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 -[ 40%] 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 -g -O2 -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 -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-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 -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-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 -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 -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -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_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 +[ 32%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.c.o +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_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 +[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.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 +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.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_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 +[ 36%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.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_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 +[ 37%] 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 -g -O2 -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 +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.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/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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.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/task.c.o -MF CMakeFiles/kalign_OBJ.dir/src/task.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/task.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/task.c -[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.c.o +[ 41%] 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/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-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 -/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; - | ^~ -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.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/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 -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.c.o -[ 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/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 -[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_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/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_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 -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_run.c.o -[ 56%] 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_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/task.c: In function 'read_tasks': -[ 58%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.c.o /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +[ 44%] 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/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 +[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.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 +[ 47%] Building C object lib/CMakeFiles/edist_utest.dir/src/euclidean_dist.c.o +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_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 +[ 48%] 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/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 +[ 50%] 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/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 +/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; + | ^~ +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.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_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 -[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.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_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 +[ 52%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.c.o +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 -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 +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_mem.c.o +[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_setup.c.o +[ 56%] 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/task_utest.dir/src/task.c.o +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 -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 +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_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: 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); @@ -1107,34 +1141,30 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] 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_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 -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.c.o +[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_controller.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_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_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 +[ 62%] 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_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 [ 63%] 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_profileprofile.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_profileprofile.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_profileprofile.c [ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o 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 CMakeFiles/kalign_OBJ.dir/src/weave_alignment.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/weave_alignment.c -[ 66%] Linking C executable alphabet_utest -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 -/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 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-sse4.1' -[ 66%] Built target alphabet_utest -[ 67%] Linking C executable task_utest +[ 66%] 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 /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 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' -[ 67%] Built target task_utest -[ 68%] Linking C executable bpm_utest +[ 66%] Built target task_utest +[ 67%] 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 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' -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' -[ 68%] Built target kalign_OBJ +/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 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 +[ 67%] 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-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 -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-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=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' @@ -1143,280 +1173,281 @@ make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-sse4.1' 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-sse4.1' -[ 70%] Linking C static library libkalign_static.a -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_static.dir/link.txt --verbose=1 -/usr/bin/ar qc libkalign_static.a CMakeFiles/kalign_OBJ.dir/src/test.c.o CMakeFiles/kalign_OBJ.dir/src/tldevel.c.o CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o CMakeFiles/kalign_OBJ.dir/src/msa_alloc.c.o CMakeFiles/kalign_OBJ.dir/src/msa_op.c.o CMakeFiles/kalign_OBJ.dir/src/msa_io.c.o CMakeFiles/kalign_OBJ.dir/src/msa_misc.c.o 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/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 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 edist_utest -[ 71%] Built target bpm_utest -[ 72%] Linking C static library libkalign.a +[ 68%] Linking C static library libkalign.a +[ 70%] Linking C executable alphabet_utest cd 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lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.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 +[ 4%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o +[ 6%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +[ 8%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o +cd 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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/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 -[ 27%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o -[ 29%] Building C object lib/CMakeFiles/tldevel.dir/src/esl_stopwatch.c.o -[ 29%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx/lib && /usr/bin/cc -DHAVE_OPENMP 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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-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 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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 -[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.c.o -[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.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 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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 -[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/alphabet.c.o -[ 43%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_check.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/tlmisc.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o.d -o 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CMakeFiles/task_utest.dir/src/tldevel.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tldevel.c +[ 25%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm.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_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-avx/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 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-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 +[ 28%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_misc.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 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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 -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.c.o -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +[ 31%] Building C object lib/CMakeFiles/bpm_utest.dir/src/bpm_test.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/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 +[ 32%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.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 +[ 33%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.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 +[ 35%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.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_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 -[ 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 -[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o +[ 36%] Building C object lib/CMakeFiles/task_utest.dir/src/tlrng.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/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 +[ 37%] Building C object lib/CMakeFiles/kalign_OBJ.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/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 -[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o +[ 39%] 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 -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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/task.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/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 +[ 41%] Building C object lib/CMakeFiles/edist_utest.dir/src/tlrng.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/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 +[ 43%] 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 -g -O2 -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 +[ 44%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bisectingKmeans.c.o +/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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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-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/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-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/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-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 -O2 -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 -[ 52%] Building C object 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/aln_wrap.c.o -MF CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/aln_wrap.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /build/reproducible-path/kalign-3.4.0/lib/src/task.c:94:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 94 | fscanf( f_ptr, "%d", &n_tasks); @@ -1424,121 +1455,181 @@ /build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_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 -[ 55%] 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 -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 +[ 45%] 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 -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 +[ 47%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/bpm.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/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 +[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/sequence_distance.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/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 +[ 50%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/euclidean_dist.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/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 /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; | ^~ +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.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/pick_anchor.c.o -MF CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/pick_anchor.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/pick_anchor.c +[ 52%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_wrap.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-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_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 +[ 54%] 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 -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 +[ 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 [ 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 -/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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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 +[ 59%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.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_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-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 +[ 62%] 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_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 -[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqseq.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_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 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 [ 64%] 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 -[ 66%] Linking C executable task_utest +[ 66%] Linking C executable alphabet_utest +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 +/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 CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +[ 67%] Linking C executable task_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 -/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 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-avx' -[ 66%] Built target task_utest -[ 67%] 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 -/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 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 -[ 68%] Linking C executable alphabet_utest -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 +/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 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 +[ 67%] Built target 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 CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest -[ 68%] Built target bpm_utest +[ 67%] Built target task_utest +[ 68%] 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 +/usr/bin/ar qc libtldevel.a CMakeFiles/tldevel.dir/src/tldevel.c.o 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-fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DNOHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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 +[ 72%] 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 +[ 74%] 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 +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/cmake -E cmake_link_script CMakeFiles/kalign.dir/link.txt --verbose=1 +[ 74%] Built target edist_utest cd 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tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/depend +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/tests /build/reproducible-path/kalign-3.4.0/obj-avx /build/reproducible-path/kalign-3.4.0/obj-avx/tests /build/reproducible-path/kalign-3.4.0/obj-avx/tests/CMakeFiles/kalign_io_test.dir/DependInfo.cmake "--color=" +[ 74%] Built target kalign_static 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 -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.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" 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tests/CMakeFiles/kalign_io_test.dir/build -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-avx' -make -f tests/CMakeFiles/kaligncpp.dir/build.make tests/CMakeFiles/kaligncpp.dir/build -make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/build +make -f src/CMakeFiles/kalignfmt.dir/build.make src/CMakeFiles/kalignfmt.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make -f tests/CMakeFiles/kalign_cmp_test.dir/build.make tests/CMakeFiles/kalign_cmp_test.dir/build +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]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' +make -f tests/CMakeFiles/dssim.dir/build.make tests/CMakeFiles/dssim.dir/build +make -f tests/CMakeFiles/kalign_lib_test.dir/build.make tests/CMakeFiles/kalign_lib_test.dir/build make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx' -[ 75%] Building C object tests/CMakeFiles/kalign_lib_test.dir/kalign_lib_test.c.o [ 75%] Building C object tests/CMakeFiles/kalign_io_test.dir/kalign_io_test.c.o -[ 75%] Building C object tests/CMakeFiles/kalign_cmp_test.dir/kalign_cmp_test.c.o -[ 77%] Building CXX object tests/CMakeFiles/kaligncpp.dir/kalign_lib_testCXX.cpp.o -cd /build/reproducible-path/kalign-3.4.0/obj-avx/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-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 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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 +[ 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 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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a /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", @@ -1552,145 +1643,146 @@ /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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] 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/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 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/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/alphabet_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/depend +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' 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/edist_utest.dir/DependInfo.cmake "--color=" +make -f lib/CMakeFiles/kalign_OBJ.dir/build.make lib/CMakeFiles/kalign_OBJ.dir/build +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/kalign_OBJ.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build 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]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' 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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make -f lib/CMakeFiles/bpm_utest.dir/build.make lib/CMakeFiles/bpm_utest.dir/build make -f lib/CMakeFiles/tldevel.dir/build.make lib/CMakeFiles/tldevel.dir/build +[ 1%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tldevel.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 +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' make[4]: Entering 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[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 2%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/test.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 make[4]: Entering directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +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/edist_utest.dir/build.make lib/CMakeFiles/edist_utest.dir/build +[ 4%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tlrng.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 -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 +[ 5%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.c.o 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 +[ 6%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.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/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-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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-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_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 +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 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-make[4]: Leaving 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 -[ 2%] Building C object lib/CMakeFiles/bpm_utest.dir/src/alphabet.c.o +[ 20%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.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 -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 -[ 4%] Building C object lib/CMakeFiles/tldevel.dir/src/tldevel.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/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/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 -[ 5%] Building C object lib/CMakeFiles/edist_utest.dir/src/tldevel.c.o +[ 21%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.c.o +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/lib && /usr/bin/cc -DHAVE_OPENMP -g -O2 -Werror=implicit-function-declaration 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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 -mavx2 -DHAVE_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 +[ 31%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_io.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 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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/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 +[ 35%] 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 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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 +[ 39%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_cmp.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 +[ 40%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/msa_sort.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 +[ 41%] Building C object lib/CMakeFiles/task_utest.dir/src/task.c.o +[ 43%] 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 -g -O2 -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 +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 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+[ 47%] 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/sequence_distance.c.o -MF CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/sequence_distance.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/sequence_distance.c /build/reproducible-path/kalign-3.4.0/lib/src/task.c: In function 'read_tasks': /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); @@ -1698,56 +1790,6 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Building C object lib/CMakeFiles/bpm_utest.dir/src/tldevel.c.o -[ 12%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/esl_stopwatch.c.o -[ 13%] Building C object lib/CMakeFiles/tldevel.dir/src/tlrng.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/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 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/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/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/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/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/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 -[ 41%] 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_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 -[ 43%] 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_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 -[ 44%] 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_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-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 /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); @@ -1755,43 +1797,49 @@ /build/reproducible-path/kalign-3.4.0/lib/src/task.c:99:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(f_ptr,"%d,%d,%d,%d,%d\n",&a->a,&a->b,&a->c,&a->p,&a->n); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.c.o +[ 48%] 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/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 +[ 50%] 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 -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 +[ 51%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/pick_anchor.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 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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 -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 +[ 54%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_param.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 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/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_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 +[ 62%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/aln_seqprofile.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 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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 -[ 48%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/weave_alignment.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-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 -[ 50%] Building C object lib/CMakeFiles/bpm_utest.dir/src/esl_stopwatch.c.o -[ 51%] Building C object lib/CMakeFiles/edist_utest.dir/src/esl_stopwatch.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 -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-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/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-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 -Wdate-time -D_FORTIFY_SOURCE=2 -mavx2 -DHAVE_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 -[ 52%] Building C object lib/CMakeFiles/alphabet_utest.dir/src/alphabet.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 -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 -[ 54%] Building C object lib/CMakeFiles/edist_utest.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 -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 -[ 55%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlrng.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/tlrng.c.o -MF CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o.d -o CMakeFiles/kalign_OBJ.dir/src/tlrng.c.o -c /build/reproducible-path/kalign-3.4.0/lib/src/tlrng.c -[ 56%] Linking C executable alphabet_utest +[ 64%] 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_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 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 +/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 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 +[ 67%] Linking C executable alphabet_utest 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 +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 CMakeFiles/alphabet_utest.dir/src/tldevel.c.o CMakeFiles/alphabet_utest.dir/src/alphabet.c.o -o alphabet_utest +[ 67%] Built target task_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 56%] Built target alphabet_utest -[ 58%] Building C object lib/CMakeFiles/tldevel.dir/src/tlmisc.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/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 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-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/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 -[ 63%] 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 -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/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 -[ 64%] Building C object lib/CMakeFiles/kalign_OBJ.dir/src/tlmisc.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/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 +[ 67%] Built target alphabet_utest +[ 68%] Linking C executable edist_utest +cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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-avx2' +[ 68%] Built target edist_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 64%] Built target kalign_OBJ +[ 68%] 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-avx2' @@ -1799,181 +1847,169 @@ 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_static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -make[4]: Leaving directory 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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 -[ 77%] Linking C executable kalign_io_test +[ 78%] 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 -[ 78%] 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/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 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/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 +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' +[ 81%] 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 -mavx2 -DHAVE_AVX2 -Wl,-z,relro -Wl,-z,now 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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a +[ 81%] Built target kalign_cmp_test +/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", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 82%] 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 +[ 83%] 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 +/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 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-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/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 +make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' +[ 91%] Building C object tests/CMakeFiles/dssim.dir/dssim_test.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 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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 +[ 94%] Built target bpm_utest make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 89%] Built target kalign_lib_test -[ 90%] Linking C executable kalign +[ 94%] Built target kaligncpp +[ 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 /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 "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/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -[ 91%] Linking C executable kalignfmt +[ 97%] 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 +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 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/13/libgomp.so 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'/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 93%] Built target kalignfmt -/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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:11:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 11 | "MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/kalign-3.4.0/tests/kalign_lib_testCXX.cpp:12:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 12 | "MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 93%] Built target largebench -[ 94%] Linking C executable dssim +[100%] Linking C executable dssim 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 -[ 95%] Linking CXX executable kaligncpp -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/tests && 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/usr/lib/gcc/x86_64-linux-gnu/13/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 95%] Built target dssim +[100%] Built target largebench make[4]: Leaving directory '/build/reproducible-path/kalign-3.4.0/obj-avx2' -[ 95%] Built target kaligncpp -[ 97%] 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 -/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 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-avx2' -[ 97%] Built target task_utest -[ 98%] Linking C executable edist_utest -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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-avx2' -[ 98%] Built target edist_utest -[100%] Linking C executable bpm_utest -cd /build/reproducible-path/kalign-3.4.0/obj-avx2/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 -mavx2 -DHAVE_AVX2 -fPIC -Wl,-z,relro -Wl,-z,now 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' -[100%] Built target bpm_utest +[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 -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 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 -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j20 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 @@ -2058,24 +2094,7 @@ 12: Working Directory: /build/reproducible-path/kalign-3.4.0/tests 12: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-07-04 15:19:48] : 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: [2025-07-04 15:19:48] : 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: [2025-07-04 15:19:53] : LOG : Timing DYN 256 -1: [2025-07-04 15:19:55] : LOG : 1.479510 - dyn -1: [2025-07-04 15:19:55] : LOG : 0.000000 - bpm -1: [2025-07-04 15:19:55] : LOG : 0.091191 - bpm_block2 -1: [2025-07-04 15:19:55] : LOG : 0.087020 - bpm_block +1: [2024-06-01 09:12:46] : LOG : Testing correctness of serial bpm. 2: LEN: 21 2: @ -1 2: A 0 @@ -2208,63 +2227,63 @@ 2: ] -1 2: ^ -1 2: _ -1 -3: [2025-07-04 15:19:48] : LOG : Check for correctness. -3: [2025-07-04 15:19:48] : LOG : Timing serial -3: [2025-07-04 15:19:48] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -4: 340 219 983 852 903 -4: 472 791 512 38 771 -4: 619 527 590 10 745 -4: 380 112 23 216 158 -4: 492 347 950 524 776 -4: 665 833 403 592 817 -4: 428 254 995 809 778 -4: 578 644 461 463 187 -4: 502 143 754 412 388 -4: 688 341 967 520 284 -4: 999 473 547 664 819 -4: 826 5 642 631 495 -4: 691 892 106 690 993 -4: 72 205 156 308 211 -4: 969 728 651 77 779 -4: 509 65 117 651 641 -4: 243 366 912 783 998 -4: 489 856 929 651 604 -4: 268 118 851 47 132 -4: 625 72 350 7 657 -4: 513 857 706 121 376 -4: 239 933 782 803 789 -4: 927 75 530 513 842 -4: 572 722 208 833 905 -4: 6 846 651 907 487 -4: 448 650 464 351 232 -4: 732 869 686 42 552 -4: 223 503 826 542 79 -4: 26 600 824 748 491 -4: 785 281 846 941 228 -4: 328 112 516 637 57 -4: 720 778 186 414 301 -4: 280 690 589 642 797 -4: 541 638 223 991 879 -4: 550 998 599 882 873 -4: 416 697 575 709 967 -4: 938 356 147 629 845 -4: 383 511 19 726 955 -4: 954 276 540 914 563 -4: 343 182 816 748 462 -4: 756 286 468 86 375 -4: 417 628 528 820 357 -4: 318 573 971 673 295 -4: 588 525 734 425 675 -4: 630 786 821 422 36 -4: 330 315 439 954 541 -4: 573 800 788 34 526 -4: 1 713 606 611 388 -4: 538 485 819 260 830 -4: 625 953 827 390 177 -4: 577 49 646 668 635 -4: 64 24 228 474 369 -4: 348 248 210 715 958 -4: 598 701 223 384 936 +3: [2024-06-01 09:12:46] : LOG : Check for correctness. +3: [2024-06-01 09:12:46] : LOG : Timing serial +3: [2024-06-01 09:12:46] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +4: 497 804 287 913 607 +4: 126 261 255 400 931 +4: 713 309 445 287 867 +4: 863 300 367 262 295 +4: 640 254 561 753 689 +4: 982 150 126 587 749 +4: 961 126 193 842 795 +4: 358 648 558 110 423 +4: 496 828 83 934 559 +4: 268 445 868 26 875 +4: 311 79 636 854 326 +4: 306 293 716 591 59 +4: 497 559 107 334 178 +4: 666 700 519 770 87 +4: 553 875 998 189 414 +4: 343 207 269 440 618 +4: 29 441 560 61 179 +4: 670 962 985 393 487 +4: 681 521 80 430 931 +4: 519 804 981 910 326 +4: 20 688 949 884 921 +4: 94 64 398 581 236 +4: 655 164 469 443 705 +4: 555 538 611 815 239 +4: 29 534 637 133 937 +4: 87 754 449 710 528 +4: 45 119 508 43 610 +4: 674 49 140 113 938 +4: 863 102 877 536 840 +4: 727 488 831 753 403 +4: 576 66 92 563 872 +4: 824 165 732 483 245 +4: 794 43 665 936 153 +4: 549 894 700 302 70 +4: 687 861 865 860 286 +4: 473 320 824 372 60 +4: 5 188 398 278 804 +4: 81 275 481 641 436 +4: 807 586 320 327 6 +4: 184 453 93 961 804 +4: 882 361 554 124 705 +4: 298 120 675 735 444 +4: 932 715 588 482 66 +4: 744 704 777 244 863 +4: 25 661 503 382 426 +4: 475 283 97 971 547 +4: 417 767 744 900 873 +4: 278 285 650 517 486 +4: 685 511 561 526 950 +4: 639 943 58 971 568 +4: 962 67 512 655 650 +4: 274 178 734 469 839 +4: 834 666 771 833 740 +4: 881 827 273 657 516 5: Aligned: 5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK @@ -2286,15 +2305,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-07-04 15:20:30] : LOG : Detected protein sequences. -6: [2025-07-04 15:20:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:20:30] : LOG : Calculating pairwise distances -6: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:20:30] : LOG : Building guide tree. -6: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:20:30] : LOG : Aligning -6: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:12:46] : LOG : Detected protein sequences. +6: [2024-06-01 09:12:46] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2024-06-01 09:12:46] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:12:46] : LOG : Calculating pairwise distances +6: [2024-06-01 09:12:46] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 +6: [2024-06-01 09:12:46] : LOG : Building guide tree. +6: [2024-06-01 09:12:46] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +6: [2024-06-01 09:12:46] : LOG : Aligning +6: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:01.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -2323,27 +2342,14 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-07-04 15:20:30] : LOG : Detected protein sequences. -7: [2025-07-04 15:20:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:20:30] : LOG : Calculating pairwise distances -7: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:20:30] : LOG : Building guide tree. -7: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:20:30] : LOG : Aligning -7: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: >1aab_ -7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG -7: KFEDMAKADKARYEREMKTYIPPKGE---------- -7: >1j46_A -7: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW -7: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK -7: >1k99_A -7: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM -7: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- -7: >2lef_A -7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA -7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK +7: [2024-06-01 09:12:46] : LOG : Detected protein sequences. +7: [2024-06-01 09:12:46] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2024-06-01 09:12:46] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2024-06-01 09:12:46] : LOG : Calculating pairwise distances +7: [2024-06-01 09:12:47] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:01.00 +7: [2024-06-01 09:12:47] : LOG : Building guide tree. +7: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +7: [2024-06-01 09:12:47] : LOG : Aligning 8: 8: Kalign (3.4.0) 8: @@ -2360,12 +2366,63 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-07-04 15:20:30] : LOG : Detected protein sequences. -8: [2025-07-04 15:20:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:20:30] : LOG : Calculating pairwise distances -8: [2025-07-04 15:20:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:20:30] : LOG : Building guide tree. +8: [2024-06-01 09:12:46] : LOG : Detected protein sequences. +8: [2024-06-01 09:12:46] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2024-06-01 09:12:46] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:12:46] : LOG : Calculating pairwise distances +8: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:01.00 +8: [2024-06-01 09:12:47] : LOG : Building guide tree. +8: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +8: [2024-06-01 09:12:47] : LOG : Aligning +8: [2024-06-01 09:12:47] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +8: >1al2_ad +8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS +8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF +8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ +8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ +8: KA--- +8: >1bbt_ac +8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- +8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF +8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY +8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- +8: ----- +8: >1bev_ac +8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N +8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC +8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG +8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ +8: TAILQ +8: >1mec_ac +8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- +8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF +8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM +8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP +8: Q---- +9: +9: Kalign (3.4.0) +9: +9: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann +9: +9: This program comes with ABSOLUTELY NO WARRANTY; for details type: +9: `kalign -showw'. +9: This is free software, and you are welcome to redistribute it +9: under certain conditions; consult the COPYING file for details. +9: +9: Please cite: +9: Lassmann, Timo. +9: "Kalign 3: multiple sequence alignment of large data sets." +9: Bioinformatics (2019) +9: https://doi.org/10.1093/bioinformatics/btz795 +9: +9: [2024-06-01 09:12:47] : LOG : Detected protein sequences. +9: [2024-06-01 09:12:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2024-06-01 09:12:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2024-06-01 09:12:47] : LOG : Calculating pairwise distances +9: [2024-06-01 09:12:47] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 +9: [2024-06-01 09:12:47] : LOG : Building guide tree. +9: [2024-06-01 09:12:47] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +9: [2024-06-01 09:12:47] : LOG : Aligning 10: 10: Kalign (3.4.0) 10: @@ -2382,39 +2439,14 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-07-04 15:20:31] : LOG : Detected protein sequences. -10: [2025-07-04 15:20:31] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-07-04 15:20:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:20:31] : LOG : Calculating pairwise distances -10: [2025-07-04 15:20:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:20:31] : LOG : Building guide tree. -10: [2025-07-04 15:20:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:20:31] : LOG : Aligning -10: [2025-07-04 15:20:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: >1al2_ad -10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -10: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -10: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -10: KA--- -10: >1bbt_ac -10: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -10: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -10: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -10: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -10: ----- -10: >1bev_ac -10: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -10: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -10: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -10: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -10: TAILQ -10: >1mec_ac -10: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -10: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -10: Q---- +10: [2024-06-01 09:12:47] : LOG : Detected protein sequences. +10: [2024-06-01 09:12:47] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2024-06-01 09:12:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:12:47] : LOG : Calculating pairwise distances +10: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +10: [2024-06-01 09:12:47] : LOG : Building guide tree. +10: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +10: [2024-06-01 09:12:47] : LOG : Aligning 11: 11: Kalign (3.4.0) 11: @@ -2431,774 +2463,19 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-07-04 15:20:31] : LOG : Detected protein sequences. -11: [2025-07-04 15:20:31] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-07-04 15:20:31] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-07-04 15:20:31] : LOG : Calculating pairwise distances - 1/12 Test #1: bpm_utest ........................ Passed 43.20 sec - 2/12 Test #2: alphabet_utest ................... Passed 43.20 sec - 3/12 Test #3: edist_utest ...................... Passed 43.20 sec - 4/12 Test #4: task_utest ....................... Passed 43.20 sec - 5/12 Test #5: C++Lib ........................... Passed 43.19 sec - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 1.48 sec - 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 1.47 sec - 8/12 Test #10: kalign_itest_BB30014.msf ......... Passed 1.47 sec -12: [2025-07-04 15:20:31] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-07-04 15:20:31] : LOG : Protein alignments - 20 seq -11: [2025-07-04 15:20:31] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 -11: [2025-07-04 15:20:31] : LOG : Building guide tree. -11: [2025-07-04 15:20:31] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 -11: [2025-07-04 15:20:31] : LOG : Aligning -11: [2025-07-04 15:20:31] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: >1ags_A -11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG -11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- -11: SKYNLY-RKDIKEK--------ALIDMYIE-GIADLGEMILLLPFTQ------------- -11: -PEEQDAKLALIKEK-IKNRYFPAFEKVLKSH--GQDYL-VGNKLSRADIHLVELLYY-- -11: -----VEE--LDSSLIS--S-FPLLKALKTRI-SNLPTVKKFLQPGSPRKPPMDEKSLEE -11: ARKIFRF------- -11: >GTA1_BOVIN -11: ----------------------------------AGKPTLHYFNGRGRMECIRWLLAAAG -11: VEFEEKFIEKPEDLDKLKNDG--SLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- -11: TKYNLY-GKDMKER--------ALIDMYSE-GVADLGEMIMHFPLCP------------- -11: -PAEKDAKLTLIREK-TTNRYLPAFENVLKSH--GQDYL-VGNKLSRADIHLVELLYY-- -11: -----VEE--LDPSLLA--N-FPLLKALKARV-SSLPAVKKFLQPGSQRKPPTDEKKIEE -11: ARKVFKF------- -11: >GTA1_MOUSE -11: ----------------------------------AGKPVLHYFNARGRMECIRWLLAAAG -11: VEFEEKFIQSPEDLEKLKKDG--NLMFDQVPMVEI-----DG--MKLAQTRAILNYIA-- -11: TKYDLY-GKDMKER--------ALIDMYSE-GILDLTEMIGQLVLCP------------- -11: -PDQREAKTALAKDR-TKNRYLPAFEKVLKSH--GQDYL-VGNRLTRVDIHLLEVLLY-- -11: -----VEE--FDASLLT--P-FPLLKAFKSRI-SSLPNVKKFLQPGSQRKPPMDAKQIQE -11: ARKAFKIQ------ -11: >GTC1_RAT -11: ----------------------------------PGKPVLHYFDGRGRMEPIRWLLAAAG -11: VEFEEQFLKTRDDLARLRNDG--SLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- -11: TKYNLY-GKDMKER--------ALIDMYAE-GVADLDEIVLHYPYIP------------- -11: -PGEKEASLAKIKDK-ARNRYFPAFEKVLKSH--GQDYL-VGNRLSRADVYLVQVLYH-- -11: -----VEE--LDPSALA--N-FPLLKALRTRV-SNLPTVKKFLQPGSQRKPLEDEKCVES -11: AVKIFS-------- -11: >GTC_RABIT -11: ----------------------------------AGKPKLHYFNARGRMESIRWLLTAAG -11: VEFEEKCMKTREDLEKLRKDG--VLMFQQVPMVEI-----DG--MKLVQTRAIFNYIA-- -11: DKHNLY-GKDIKER--------ALIDMYTE-GIVDLNELILTRPFLP------------- -11: -PEEQEAKLAQIKDK-AKNRYFPAFEKVLKSH--GQDYL-VGNKLSKADILLVELLYN-- -11: -----VEE--LNPGATA--S-FPLLQALKTRI-SNLPTVKKFLQPGSQRNPPDDEKCREE -11: AKIIFH-------- -11: >GTA1_RABIT -11: ---------------------------------MARKPLLHYFNGRGRMESIRWLLAAAG -11: EEFDEKFMETAEDLDKLRNDG--SLMYQQVPMVEI-----DG--MKLVQTRAILNYVA-- -11: NKHNLY-GKDMKER--------ALIDMYTE-GVADLYELVLLLPLCP------------- -11: -PEQKDAKVDFIKEK-IRTRYFPAFEKVLKSH--GQDYL-VGNRLSKADILLVELLYN-- -11: -----VEE--LDPSAIA--S-FPLLKALKTRI-SSLPTVKKFLQPGSQRKPPMDEKNLEK -11: AKKIFKIP------ -11: >GTA1_CAVPO -11: ----------------------------------SGKPVLHYFNVQGRMESIRWLLAAAG -11: VEFEEKLIMCQEDLDKLKNDG--LLMFQQVPMVEM-----DG--MKMVQSRAILNYIA-- -11: TKYNLY-GKDTKER--------LLIDMYTE-GMTDLYELFFKVILAP------------- -11: -PEEKDAAKSLIKDR-AKNRFLPAFEKVLKSH--GQGYL-VGNKLSKADILLTELLYM-- -11: -----VEE--FDASLLA--N-FTLLQALKTRV-SNLPNVKKFLQPGSQRKPFPTQEMFEE -11: MRKF---------- -11: >GTA3_RAT -11: ---------------------------------MEVKPKLYYFQGRGRMESIRWLLATAG -11: VEFEEEFLETREQYEKLQKDG--CLLFGQVPLVEI-----DG--MLLTQTRAILSYLA-- -11: AKYNLY-GKDLKER--------VRIDMYAD-GTQDLMMMIIGAPFKA------------- -11: -PQEKEESLALAVKR-AKNRYFPVFEKILKDH--GEAFL-VGNQLSWADIQLLEAILM-- -11: -----VEE--VSAPVLS--D-FPLLQAFKTRI-SNIPTIKKFLQPGSQRKPPPDGHYVDV -11: VRTVLKF------- -11: >GTA3_CHICK -11: ----------------------------------AAKPVLYYFNGRGKMESIRWLLAAAG -11: VEFEEVFLETREQYEKLLQSG--ILMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- -11: GKYNLY-GKDLKER--------ALIDMYVG-GTDDLMGFLLSFPFLS------------- -11: -AEDKVKQCAFVVEK-ATSRYFPAYEKVLKDH--GQDFL-VGNRLSWADIHLLEAILM-- -11: -----VEE--KKSDALS--G-FPLLQAFKKRI-SSIPTIKKFLAPGSKRKPISDDKYVET -11: VRRVLRMYYDVKPH -11: >GTA2_CHICK -11: ---------------------------------MAGKPKLHYTRGRGKMESIRWLLAAAG -11: VEFEEEFIEKKEDLEKLRNDG--SLLFQQVPMVEI-----DG--MKMVQSRAILCYIA-- -11: GKYNLY-GKDLKER--------AWIDMYVE-GTTDLMGMIMALPFQA------------- -11: -ADVKEKNIALITER-ATTRYFPVYEKALKDH--GQDYL-VGNKLSWADIHLLEAILM-- -11: -----TEE--LKSDILS--A-FPLLQAFKGRM-SNVPTIKKFLQPGSQRKPPLDEKSIAN -11: VRKIFSF------- -11: >GTA1_CHICK -11: ---------------------------------MSGKPVLHYANTRGRMESVRWLLAAAG -11: VEFEEKFLEKKEDLQKLKSDG--SLLFQQVPMVEI-----DG--MKMVQTRAILNYIA-- -11: GKYNLY-GKDLKER--------ALIDMYVE-GLADLYELIMMNVVQP------------- -11: -ADKKEEHLANALDK-AANRYFPVFEKVLKDH--GHDFL-VGNKLSRADVHLLETILA-- -11: -----VEE--SKPDALA--K-FPLLQSFKART-SNIPNIKKFLQPGSQRKPRLEEKDIPR -11: LMAIFH-------- -11: >GTA1_ANTST -11: ---------------------------------MAGEQNIKYFNIKGRMEAIRWLLAVAG -11: VEFEEKFFETKEQLQKLKET---VLLFQQVPMVEI-----DG--MKLVQTRAILHYIA-- -11: EKYNLL-GKDMKEH--------AQIIMYSE-GTMDLMELIMIYPFLK------------- -11: -GEEKKQRLVEIANK-AKGRYFPAFENVLKTH--GQNFL-VGNQLSMADVQLFEAILM-- -11: -----VEE--KVPDALS--G-FPLLQAFKTRI-SNIPTVKTFLAPGSKRKPVPDAKYVED -11: IIKIFYF------- -11: >GTA4_HUMAN -11: ---------------------------------MAARPKLHYPNGRGRMESVRWVLAAAG -11: VEFDEEFLETKEQLYKLQDGN--HLLFQQVPMVEI-----DG--MKLVQTRSILHYIA-- -11: DKHNLF-GKNLKER--------TLIDMYVE-GTLDLLELLIMHPFLK------------- -11: -PDDQQKEVVNMAQK-AIIRYFPVFEKILRGH--GQSFL-VGNQLSLADVILLQTILA-- -11: -----LEE--KIPNILS--A-FPFLQEYTVKL-SNIPTIKRFLEPGSKKKPPPDEIYVRT -11: VYNIFRP------- -11: >1oe7_A -11: -----------------------------------DHIKVIYFNGRGRAESIRMTLVAAG -11: VNYEDERISF-QDWPKIKP----TIPGGRLPAVKITDNHGHV--KWMVESLAIARYMA-- -11: KKHHMM-GGTEEEY--------YNVEKLIG-QAEDLEHEYYKTLMKP------------- -11: -EEEKQKIIKEILNG-KVPVLLDIICESLKAS--TGKLA-VGDKVTLADLVLIAVIDH-- -11: -----VTD--LDKEFLT--GKYPEIHKHRENLLASSPRLAKYL---SDRA---------- -11: -------------- -11: >GTP1_BUFBU -11: -----------------------------------PEYTIIYFNARGRCEAMRMLMADQG -11: AQWKEEVVTS-DDWQKGDLKK--AAVYGQLPGFK------DGD-FTLYQSNAMLRLLA-- -11: RNHDLY-GKNPREA--------SLIDMVND-GVEDLRLKYLKMIYQN------------- -11: -YENGKDDYV----K-ALPTNLGHFERLLASNNEGKGFV-VGAHISFADYNLVDLLHN-- -11: -----HLV--LAPDCLS--G-FPLLCAYVKRI-SSRPKLEAYLSSDAHKKRPINGNGKQQ -11: -------------- -11: >GT28_SCHJA -11: -------------------------------------VKLIYFNGRGRAEPIRMILVAAG -11: VEFEDERIEF-QDWPKIKP----TIPGGRLPIVKITDKRGDV--KTMSESLAIARFIA-- -11: RKHNMM-GDTDDEY--------YIIEKMIG-QVEDVESEYHKTLIKP------------- -11: -PEEKEKISKEILNG-KVPILLQAICETLKES--TGNLT-VGDKVTLADVVLIASIDH-- -11: -----ITD--LDKEFLT--GKYPEIHKHRKHLLATSPKLAKYL---SERHATAF------ -11: -------------- -11: >GTS1_ASCSU -11: -----------------------------------PQYKLTYFDIRGLGEGARLIFHQAG -11: VKFEDNRLKR-EDWPALKP----KTPFGQLPLLEV-----DGE--VLAQSAAIYRYLG-- -11: RQFGLA-GKTPMEE--------AQVDSIFD-QFKDFMAELRPC-FRV-----LAGFE--- -11: -EGDKEKVLKEVAVP-ARDKHLPLLEKFLA--KSGSEYM-VGKSVTWADLVITDSLAS-- -11: -----WES--LIPDFLS--G-HLQLKKYIEHV-RELPNIKKWIAERPKTPY--------- -11: -------------- -11: >GTS9_CAEEL -11: ----------------------------------MVSYKLIYFQSRGNGEIARQVFAFAG -11: QEFIDERISK-EQWAEIKN----MTPFGQVPVLEV-----DGR--QLAQSITIVRYLS-- -11: KQFGIS-GKSSWEE--------AQVDALGD-QFKDYRVEARPF-FRA-----KMGFS--- -11: -DGDVDQLYKDLFVP-AFNKMYSIFTESLK--SSGSGFL-VGDSLTWMDLAIAQHSAD-- -11: -----LLE--ADGKILD--T-FLEMKDHQKKI-HSIPNVKKWIEKRPVTSR--------- -11: -------------- -11: >GTS3_CAEEL -11: ----------------------------------MVHYKLTYFNARGLAEISRQLFHMAG -11: VEFEDERINE-EKFSQLKP----TFPSGQVPILCI-----DGA--QFSQSTAIARYLA-- -11: RKFGFV-GQTAEEE--------LQADEVVD-TFKDFIESFRKFVIAV-----LSGES--- -11: -EEILKNIREEVIKP-AVKTYTAYLKAILE--KSSSGYL-VGNELTWADLVIADNLTT-- -11: -----LIN--AELLDIE--N-DKLLKEFREKI-IETPKLKEWLAKRPETRF--------- -11: -------------- -11: >GTS5_CAEEL -11: ----------------------------------MVSYKLTYFNGRGAGEVSRQIFAYAG -11: QQYEDNRVTQ-EQWPALKETC--AAPFGQLPFLEV-----DGK--KLAQSHAIARFLA-- -11: REFKLN-GKTAWEE--------AQVNSLAD-QYKDYSSEARPY-FYA-----VMGFG--- -11: -PGDVETLKKDIFLP-AFEKFYGFLVNFLK--ASGSGFL-VGDSLTWIDLAIAQHSAD-- -11: -----LI---AKGGDFS--K-FPELKAHAEKI-QAIPQIKKWIETRPVTPF--------- -11: -------------- -11: >GTS6_CAEEL -11: ----------------------------------MVHYKLVYFPLRARAEIARQIFAYAG -11: QDYSEENLSF-EQWPARKN----NTPFGQLPILEV-----DGK--PLGQSYAIARYLA-- -11: REFGIA-GQNDTEA--------AEVDAIAD-QFKDYLNDVSPY-LTV-----LAGFK--- -11: -PGDKDQLRTDVFVP-AFKKNFEFFENILA--SNHSGFF-VGNSLTWVDLLISQHVQD-- -11: -----ILD--KDLAVVE--E-FKKVLAHRKKV-QSIDRIQKYIANRPDYPF--------- -11: -------------- -11: >GTS4_CAEEL -11: ----------------------------------MPNYKLLYFDARALAEPIRIMFAMLN -11: VPYEDYRVSV-EEWSKLKP----TTPFGQLPILQV-----DGE--QFGQSMSITRYLA-- -11: RKFGLA-GKTAEEE--------AYADSIVD-QYRDFIFFFRQFTSSV-----FYGSD--- -11: -ADHINKVRFEVVEP-ARDDFLAIINKFLA--KSKSGFL-VGDSLTWADIVIADNLTS-- -11: -----LLK--NGFLDFN--K-EKKLEEFYNKI-HSIPEIKNYVATRKDSIV--------- -11: -------------- -11: >GTS2_CAEEL -11: ----------------------------------MVHYKLMCFDVRGLGEVIRQLFYLGD -11: VSFEDFRVSR-EEFKSLKS----NLPSGQLPVLEI-----DGV--MISQSASIGRFLA-- -11: RQYGYS-GKTPTEE--------MQVDSIID-LFKDFMLTFRQFFFAV-----IHGYP--- -11: -EYEKERMKRDIVKP-AIKNYFIALNKILL--RSKSGFL-VGDDLTWADLQIADNLST-- -11: -----LIN--IRLF-AE--K-EPHLNVFIRKL---------------------------- -11: -------------- -11: >GTS1_CAEEL -11: ----------------------------------MPHFKFYYFDVRGRGEAIRLLFHLAD -11: EKFDDERFGM-EQWGVLKS----EMPLGQVPVLEI-----DGV--KISQTTAIARYLG-- -11: HQFHRA-GTNAVDC--------ARLDMIAE-VIQEFMSSSGMGKFSR----VLLGMI--- -11: -QANKEQFFKENVLP-DVEKYAPIVEKFLL-ENGNNGLL-LGDRETWVDVFAAESFSK-- -11: -----LIDY-GSPDALD--A-YPHILALINRV-FNHPNIKKYVSQRKATPA--------- -11: -------------- -11: >GTS_ANOGA -11: -------------------LSSSSISRSSLKCNIMPDYKVYYFNVKALGEPLRFLLSYGN -11: LPFDDVRITR-EEWPALKP----TMPMRQMPVLEV-----DGK--RVHQSLAMCRYVA-- -11: KQINLA-GDNPLEA--------LQIDAIVD-TINDFRLKIAIVAYEP------DDMV--- -11: -KEKKMVTLNNEVIPFYLTKLNVIAKE-------NNGHL-VLGKPTWADVYFAGILDY-- -11: -----L-NYLTKTNLLE--N-FPNLQEVVQKV-LDNENVKAYIAKRPITEV--------- -11: -------------- -11: >GTS2_MANSE -11: ----------------------------------MPKVVFHYFGAKGWARP-TMLLAYGG -11: QEFEDHRVEY-EQWPEFKP----NTPFGQMPVLEI-----DGK--KYAQSLAISRYLG-- -11: RKYGLA-GNDIEED--------FEIDQIVD-FVNDIRASAASVEYEQ------DAAN--- -11: -KEVKHEENMKNKYPFQLNKLSEIITK-------NNGFL-ALGRLTWADFVFVGMFDY-- -11: -----LKKMLRMPDLEE--Q-YPIFKKPIETV-LSNPKLKAYLDSAPKKEF--------- -11: -------------- -11: >GT1_ONCVO -11: FITMNFVVEAASSNANQAITSENSIKPKGKLQPQMEKYTLTYFNGRGRAEVIRLLFALAN -11: VSYEDNRITR-DEWKYLKP----RTPFGHVPMLNV-----SGN--VLGESHAIELLLG-- -11: GRFGLL-GTNDWEE--------AKIMAVVL-NIDELFQKLIPWTHEK-----NTTKK--- -11: -AELFRNLSESDVMP-FLGRY----EKFLK--ESTTGHI-VGNKVSVADLTVFNMLMT-- -11: -----L----DDEVKLE--E-YPQLASFVNKI-GQMPGIKEWIKKRPKTYF--------- -11: -------------- -11: >SC11_OMMSL -11: ----------------------------------MPSYTLYYFNGRGRAEICRMLFAVAS -11: VQYQDKRIEL-AEWTQFKT----KMPCHMLPILEI-----DTE-TQVPQSMAISRYLA-- -11: REFGFY-GKNNMDM--------FKVDCLCD-SLFELFNDYMAVYNEK------------- -11: -DAAKKTELQKRFQN-TCLRVLPYMEKTLEANKGGAGWF-IGDQILLCDMMTHAALEN-- -11: -----PIQ--ENANLLK--E-YPKLAALRTRV-AAHPKIAAYIKKRNNTAF--------- -11: -------------- -11: >SC2_OCTDO -11: ----------------------------------MPSYTLNYFNHRGRAEICRMLFAAAG -11: VQYNDRRIET-SEWSNMRS----KMPCSMMPMLDI-----DNR-HQIPQTMAIARYLA-- -11: REFGFH-GKNNMEM--------ARVEYISD-CFYDILDDYLRMYQDDNCRMMFQRSG--- -11: -DRNGSSEKRTRYQE-TLRRILPFMERTLEMYKSGGQFF-MGDQMTMADMMCYCALEN-- -11: -----PIM--EESSLLN--S-YPKLQALRTRV-MSHLKMSPYLKKRSSTEF--------- -11: -------------- -11: >1aw9_ -11: ----------------------------------AP-LKLYGMPLSPNVVRVATVLNEKG -11: LDFEIVPVDLTTGAHKQPDFL-ALNPFGQIPALV------DGD-EVLFESRAINRYIA-- -11: SKYASE-GTDLLPATASA----AKLEVWLEVESHHFYPNASPLVFQL----LVRPLL--- -11: -GGAPDAAVVDKHAE-QLAKVLDVYEAHLA----RNKYL-AGDEFTLADANHASYLLY-- -11: -----L-SKTPKAGLVA--A-RPHVKAWWEAI-VARPAFQKTVAAIPLPPPP-------- -11: -------------- -11: >GTH3_ARATH -11: -----------------------------------V-LTIYA-PLFASSKRAVVTLVEKG -11: VSFETVNVDLMKGEQRQPEYL-AIQPFGKIPVLV------DGD-YKIFESRAIMRYIA-- -11: EKYRSQ-GPDLLGKTIEER---GQVEQWLDVEATSYHPPLLALTLNI----VFAPLM--- -11: -GFPADEKVIKESEE-KLAEVLDVYEAQLS----KNEYL-AGDFVSLADLAHLPFTEY-- -11: -----LVGPIGKAHLIK--D-RKHVSAWWDKI-SSRAAWKEVSAKYSLPV---------- -11: -------------- -11: >GTH7_ARATH -11: ----------------------------------MV-VKVYGQIKAANPQRVLLCFLEKD -11: IEFEVIHVDLDKLEQKKPQHL-LRQPFGQVPAIE------DGY-LKLFESRAIARYYA-- -11: TKYADQ-GTDLLGKTLEGR---AIVDQWVEVENNYFYAVALPLVMNV----VFKPKS--- -11: -GKPCDVALVEELKV-KFDKVLDVYENRLA----TNRYL-GGDEFTLADLSHMPGMRY-- -11: -----IMNETSLSGLVT--S-RENLNRWWNEI-SARPAWKKLMELAAY------------ -11: -------------- -11: >GTH6_ARATH -11: ---------------------------------MAS-IKVHGVPMSTATMRVLATLYEKD -11: LQFELIPVDMRAGAHKQEAHL-ALNPFGQIPALE------DGD-LTLFESRAITQYLA-- -11: EEYSEK-GEKLISQDCKKVK--ATTNVWLQVEGQQFDPNASKLAFER----VFKGMF--- -11: -GMTTDPAAVQELEG-KLQKVLDVYEARLA----KSEFL-AGDSFTLADLHHLPAIHY-- -11: -----LLGTDSKV-LFD--S-RPKVSEWIKKI-SARPAWAKVIDLQKQ------------ -11: -------------- -11: >GTH_SILCU -11: -----------------------------------T-IKVHGNPRSTATQRVLVALYEKH -11: LEFEFVPIDMGAGGHKQPSYL-ALNPFGQVPALE------DGE-IKLFESRAITKYLAYT -11: HDHQNE-GTSLIHKE-KHEM--AAQLVWEEVEAHQFDPVASKLAWEL----VFKGIF--- -11: -GMQTDTTVVEENEA-KLAKVLDVYEARLT----ESEYLGANDSFTLVDLHHLPLLGY-- -11: -----LMGTQVKK-LFE--E-RAHVSAWCKKI-LARPSWEKTLALQKQA----------- -11: -------------- -11: >GTH1_ARATH -11: ---------------------------------MAG-IKVFGHPASTATRRVLIALHEKN -11: VDFEFVHVELKDGEHKKEPFI-LRNPFGKVPAFE------DGD-FKIFESRAITQYIA-- -11: HEFSDK-GNNLLST-GKDM---AIIAMGIEIESHEFDPVGSKLVWEQ----VLKPLY--- -11: -GMTTDKTVVEEEEA-KLAKVLDVYEHRLG----ESKYL-ASDHFTLVDLHTIPVIQY-- -11: -----LLGTPTKK-LFD--E-RPHVSAWVADI-TSRPSAQKVL----------------- -11: -------------- -11: >GTH4_ARATH -11: ----------------------------------AG-IKVFGHPASIATRRVLIALHEKN -11: LDFELVHVELKDGEHKKEPFL-SRNPFGQVPAFE------DGD-LKLFESRAITQYIA-- -11: HRYENQ-GTNLLQTDSKNISQYAIMAIGMQVEDHQFDPVASKLAFEQ----IFKSIY--- -11: -GLTTDEAVVAEEEA-KLAKVLDVYEARLK----EFKYL-AGETFTLTDLHHIPAIQY-- -11: -----LLGTPTKK-LFT--E-RPRVNEWVAEI-TKRPASEKVQ----------------- -11: -------------- -11: >GTH4_MAIZE -11: ---------------------------------ATPAVKVYGWAISPFVSRALLALEEAG -11: VDYELVPMSRQDGDHRRPEHL-ARNPFGKVPVLE------DGD-LTLFESRAIARHVL-- -11: RKHKP----ELLGGGR-LEQT-AMVDVWLEVEAHQLSPPAIAIVVEC----VFAPFL--- -11: -GRERNQAVVDENVE-KLKKVLEVYEARLA----TCTYL-AGDFLSLADLSPFTIMHC-- -11: -----LMATEYAA-LVH--A-LPHVSAWWQGL-AARPAANKVAQFMPVGAGAPKEQE--- -11: -------------- -11: >GTH1_MAIZE -11: ---------------------------------A-P-MKLYGAVMSWNLTRCATALEEAG -11: SDYEIVPINFATAEHKSPEHL-VRNPFGQVPALQ------DGD-LYLFESRAICKYAA-- -11: RKNKP----ELLREGN-LEEA-AMVDVWIEVEANQYTAALNPILFQV----LISPML--- -11: -GGTTDQKVVDENLE-KLKKVLEVYEARLT----KCKYL-AGDFLSLADLNHVSVTLC-- -11: -----LFATPYAS-VLD--A-YPHVKAWWSGL-MERPSVQKVAALMKPSA---------- -11: -------------- -11: >GTH1_WHEAT -11: ---------------------------------MSP-VKVFGHPMLTNVARVLLFLEEVG -11: AEYELVPMDFVAGEHKRPQHV-QLNPFAKMPGFQ------DGD-LVLFESRAIAKYIL-- -11: RKYGGTAGLDLLGENSGIEEL-AMVDVWTEVEAQQYYPAISPVVFEC----IIIPFIIPG -11: GGAAPNQTVVDESLE-RLRGVLGIYEARLE----KSRYL-AGDSITFADLNHIPFTFY-- -11: -----FMTTPYAK-VFD--D-YPKVKAWWEML-MARPAVQRVCKHMPTEFKLGAQY---- -11: -------------- -11: >GTH5_ARATH -11: ---------------------------------MVT-VKLYGMAYSTCTKRVYTTAKEIG -11: VDVKIVPVDLMKGEHKEPAYLDNYHPFGVIPVLE------DEDGTKIYESRAISRYLV-- -11: AKYGK--GSSLLPSPSDPKAY-GLFEQAASVEYSSFDPPASSLAYER----VFAGMR--- -11: -GLKTNEELAKKYVD-TLNAKMDGYERILS----KQKYL-AGNDFTLADLFHLPY-GA-- -11: -----MVAQLEPT-VLD--S-KPHVKAWWAA--SLRVIPGRLLRNSSKEFM--------- -11: -------------- -11: >1eem_A -11: ---------------SARSLGKGSAPPGPV---PEGSIRIYSMRFCPFAERTRLVLKAKG -11: IRHEVININLKNKPEWFFK----KNPFGLVPVLENS----QGQ--LIYESAITCEYLD-- -11: EAYP---GKKLLPDDPYEK---ACQKMILE-LFSKVPSLVGSFIRSQ------------- -11: -N-KEDYAGLKE----EFRKEFTKLEEVLTNK--KTTFF-GGNSISMIDYLIWPWFER-- -11: -----LEAM-KLNECVD--H-TPKLKLWMAAM-KEDPTVSALLTSEKDWQGFLE-LYLQN -11: SPEACDYGL----- -11: >GTO1_MOUSE -11: -----------MSGESSRSLGKGSAPPGPV---PEGQIRVYSMRFCPFAQRTLMVLKAKG -11: IRHEVININLKNKPEWFFE----KNPLGLVPVLENS----QGH--LVTESVITCEYLD-- -11: EAYP---EKKLFPDDPYKK---ARQKMTLE-SFSKVPPLIASFVRSK------------- -11: -R-KEDSPNLRE----ALENEFKKLEEGMDNY--K-SFL-GGDSPSMVDYLTWPWFQR-- -11: -----LEAL-ELKECLA--H-TPKLKLWMAAM-QQDPVASSHKIDAKTYREYLN-LYLQD -11: SPEACDYGL----- -11: >GTO2_HUMAN -11: -----------MSGDATRTLGKGSQPPGPV---PEGLIRIYSMRFCPYSHRTRLVLKAKD -11: IRHEVVNINLRNKPEWYYT----KHPFGHIPVLETS----QCQ--LIYESVIACEYLD-- -11: DAYP---GRKLFPYDPYER---ARQKMLLE-LFCKVPHLTKECLVAL------------- -11: -RCGRECTNLKA----ALRQEFSNLEEILEYQ--NTTFF-GGTCISMIDYLLWPWFER-- -11: -----LDVY-GILDCVS--H-TPALRLWISAM-KWDPTVCALLMDKSIFQGFLN-LYFQN -11: NPNAFDFGLC---- -11: >YKJ3_CAEEL -11: -------------------MTVLAGVNSKIVKNGCWNHSYLQHAILPVAQRALIYASVKN -11: IPSDVINVHLQEKPDWYFS----KHYKGQVPTLEHD----EGK-KHVIESAVIPEYLD-- -11: DIYP---ETRILPTDPYEK---VQQKLLLDRISGQVSPAFYGVVQAV------------- -11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY -11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS -11: PNYDYGLTKLSETI - 9/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.05 sec -9: -9: Kalign (3.4.0) -9: -9: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -9: -9: This program comes with ABSOLUTELY NO WARRANTY; for details type: -9: `kalign -showw'. -9: This is free software, and you are welcome to redistribute it -9: under certain conditions; consult the COPYING file for details. -9: -9: Please cite: -9: Lassmann, Timo. -9: "Kalign 3: multiple sequence alignment of large data sets." -9: Bioinformatics (2019) -9: https://doi.org/10.1093/bioinformatics/btz795 -9: -9: [2025-07-04 15:20:33] : LOG : Detected protein sequences. -9: [2025-07-04 15:20:33] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-07-04 15:20:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:03.00 -9: [2025-07-04 15:20:33] : LOG : Calculating pairwise distances -9: [2025-07-04 15:20:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:20:33] : LOG : Building guide tree. -9: [2025-07-04 15:20:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:20:33] : LOG : Aligning -9: [2025-07-04 15:20:33] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: >1al2_ad -9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -9: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -9: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -9: KA--- -9: >1bbt_ac -9: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -9: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -9: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -9: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -9: ----- -9: >1bev_ac -9: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -9: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -9: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -9: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -9: TAILQ -9: >1mec_ac -9: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -9: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -9: Q---- -10/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 3.15 sec -8: [2025-07-04 15:20:37] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:07.00 -8: [2025-07-04 15:20:37] : LOG : Aligning -8: [2025-07-04 15:20:37] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: >1al2_ad -8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -8: KA--- -8: >1bbt_ac -8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -8: ----- -8: >1bev_ac -8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -8: TAILQ -8: >1mec_ac -8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -8: Q---- -11/12 Test #8: kalign_itest_BB12006.msf ......... 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:21:17] : LOG : Protein alignments - 1000 seq -12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:21:38] : LOG : Protein alignments - 10000 seq -12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-07-04 15:21:50] : LOG : DNA alignments - 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:22:03] : LOG : DNA alignments - 1000 seq -12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:22:18] : LOG : DNA alignments - 10000 seq -12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 115.81 sec - -100% tests passed, 0 tests failed out of 12 - -Total Test time (real) = 159.01 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' -set -e ; for SIMD in avx2 avx sse4.1 ; do \ - if lscpu | grep -q ${SIMD} ; then \ - cd "obj-${SIMD}/" && \ - ctest --verbose ; \ - cd .. ; \ - fi ; \ -done -UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl -Parse Config file:/build/reproducible-path/kalign-3.4.0/obj-avx2/DartConfiguration.tcl -Test project /build/reproducible-path/kalign-3.4.0/obj-avx2 -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -test 1 - Start 1: bpm_utest - -1: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/bpm_utest -1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib -1: Test timeout computed to be: 1500 -1: LEN: 256 -1: [2025-07-04 15:22:32] : 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: [2025-07-04 15:22:32] : 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: [2025-07-04 15:22:41] : LOG : Timing DYN 256 -1: [2025-07-04 15:22:42] : LOG : 1.476655 - dyn -1: [2025-07-04 15:22:42] : LOG : 0.057554 - bpm -1: [2025-07-04 15:22:42] : LOG : 0.090745 - bpm_block2 -1: [2025-07-04 15:22:42] : LOG : 0.112721 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 10.30 sec -test 2 - Start 2: alphabet_utest - -2: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib/alphabet_utest -2: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx2/lib -2: Test timeout computed to be: 1500 -2: LEN: 21 -2: @ -1 -2: A 0 -2: B 20 -2: C 1 -2: D 2 -2: E 3 -2: F 4 -2: G 5 -2: H 6 -2: I 7 -2: J -1 -2: K 8 -2: L 9 -2: M 10 -2: N 11 -2: O -1 -2: P 12 -2: Q 13 -2: R 14 -2: S 15 -2: T 16 -2: U 20 -2: V 17 -2: W 18 -2: X 20 -2: Y 19 -2: Z 20 -2: [ -1 -2: \ -1 -2: ] -1 -2: ^ -1 -2: _ -1 -2: LEN: 13 -2: @ -1 -2: A 0 -2: B 2 -2: C 1 -2: D 2 -2: E 3 -2: F 4 -2: G 5 -2: H 6 -2: I 7 -2: J -1 -2: K 8 -2: L 9 -2: M 9 -2: N 2 -2: O -1 -2: P 10 -2: Q 3 -2: R 8 -2: S 0 -2: T 0 -2: U -1 -2: V 7 -2: W 11 -2: X 12 -2: Y 4 -2: Z 3 -2: [ -1 -2: \ -1 -2: ] -1 -2: ^ -1 -2: _ -1 -2: LEN: 5 -2: @ -1 -2: A 0 -2: B 4 -2: C 1 -2: D 4 -2: E -1 -2: F -1 -2: G 2 -2: H 4 -2: I -1 -2: J -1 -2: K 4 -2: L -1 -2: M 4 -2: N 4 -2: O -1 -2: P -1 -2: Q -1 -2: R 4 -2: S 4 -2: T 3 -2: U 3 -2: V 4 -2: W 4 -2: X -1 -2: Y 4 -2: Z -1 -2: [ -1 -2: \ -1 -2: ] -1 -2: ^ -1 -2: _ -1 -2: LEN: 6 -2: @ -1 -2: A 0 -2: B 5 -2: C 1 -2: D 2 -2: E 2 -2: F 1 -2: G 3 -2: H 3 -2: I 1 -2: J -1 -2: K 2 -2: L 4 -2: M 0 -2: N 2 -2: O -1 -2: P 2 -2: Q 2 -2: R 2 -2: S 3 -2: T 3 -2: U -1 -2: V 1 -2: W 4 -2: X 5 -2: Y 4 -2: Z 5 -2: [ -1 -2: \ -1 -2: ] -1 -2: ^ -1 -2: _ -1 - 2/12 Test #2: alphabet_utest ................... Passed 0.00 sec -test 3 - Start 3: edist_utest - -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: [2025-07-04 15:22:42] : LOG : Check for correctness. -3: [2025-07-04 15:22:42] : LOG : Timing serial -3: [2025-07-04 15:22:42] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -3: [2025-07-04 15:22:42] : LOG : Timing AVX -3: [2025-07-04 15:22:42] : 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 - -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: 115 228 589 931 505 -4: 532 193 925 139 462 -4: 98 644 758 517 706 -4: 198 298 518 559 187 -4: 148 877 520 709 906 -4: 709 6 762 299 582 -4: 212 601 172 122 278 -4: 321 822 73 488 212 -4: 164 768 796 585 199 -4: 583 856 306 964 560 -4: 206 977 149 435 20 -4: 508 337 252 576 221 -4: 537 684 820 910 267 -4: 813 213 893 470 871 -4: 916 114 973 402 583 -4: 937 687 91 181 370 -4: 847 859 77 659 998 -4: 413 997 114 802 5 -4: 719 393 386 468 657 -4: 384 370 21 813 394 -4: 739 244 155 2 846 -4: 167 73 712 636 797 -4: 493 282 510 169 719 -4: 497 280 366 116 30 -4: 396 667 506 994 558 -4: 416 170 580 29 822 -4: 382 76 778 674 73 -4: 686 563 724 708 482 -4: 195 247 703 766 82 -4: 839 51 143 596 925 -4: 344 350 660 861 867 -4: 349 584 464 56 606 -4: 275 91 127 668 642 -4: 507 992 19 526 3 -4: 901 930 647 433 848 -4: 288 183 142 661 15 -4: 578 723 96 546 533 -4: 652 873 726 341 800 -4: 752 143 981 952 187 -4: 935 992 716 843 345 -4: 249 844 587 827 426 -4: 412 281 431 456 759 -4: 288 85 881 686 844 -4: 296 916 565 557 363 -4: 163 706 160 578 466 -4: 983 969 132 923 455 -4: 477 504 994 156 318 -4: 151 209 0 166 703 -4: 567 200 942 574 843 -4: 295 61 561 400 120 -4: 494 283 471 829 565 -4: 985 51 552 204 999 -4: 19 577 450 479 550 -4: 518 123 374 639 397 - 4/12 Test #4: task_utest ....................... Passed 0.00 sec -test 5 - Start 5: C++Lib - -5: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/tests/kaligncpp -5: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -5: Test timeout computed to be: 1500 -5: Aligned: -5: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE---------- -5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK -5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- -5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 5/12 Test #5: C++Lib ........................... Passed 0.00 sec -test 6 - Start 6: kalign_itest_BB11001.tfa - -6: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa" -6: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -6: Test timeout computed to be: 1500 -6: -6: Kalign (3.4.0) -6: -6: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -6: -6: This program comes with ABSOLUTELY NO WARRANTY; for details type: -6: `kalign -showw'. -6: This is free software, and you are welcome to redistribute it -6: under certain conditions; consult the COPYING file for details. -6: -6: Please cite: -6: Lassmann, Timo. -6: "Kalign 3: multiple sequence alignment of large data sets." -6: Bioinformatics (2019) -6: https://doi.org/10.1093/bioinformatics/btz795 -6: -6: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -6: [2025-07-04 15:22:42] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -6: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:22:42] : LOG : Building guide tree. -6: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:22:42] : LOG : Aligning -6: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: >1aab_ -6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG -6: KFEDMAKADKARYEREMKTYIPPKGE---------- -6: >1j46_A -6: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKW -6: PFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK -6: >1k99_A -6: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKM -6: KYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- -6: >2lef_A -6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA -6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.01 sec -test 7 - Start 7: kalign_itest_BB11001_EOF.msf - -7: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf" -7: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -7: Test timeout computed to be: 1500 -7: -7: Kalign (3.4.0) -7: -7: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -7: -7: This program comes with ABSOLUTELY NO WARRANTY; for details type: -7: `kalign -showw'. -7: This is free software, and you are welcome to redistribute it -7: under certain conditions; consult the COPYING file for details. -7: -7: Please cite: -7: Lassmann, Timo. -7: "Kalign 3: multiple sequence alignment of large data sets." -7: Bioinformatics (2019) -7: https://doi.org/10.1093/bioinformatics/btz795 -7: -7: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -7: [2025-07-04 15:22:42] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -7: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:22:42] : LOG : Building guide tree. -7: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:22:42] : LOG : Aligning -7: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2024-06-01 09:12:47] : LOG : Detected protein sequences. +11: [2024-06-01 09:12:47] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2024-06-01 09:12:47] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2024-06-01 09:12:47] : LOG : Calculating pairwise distances +12: [2024-06-01 09:12:47] : LOG : DSSim - a simplistic sequence simulator. +12: [2024-06-01 09:12:47] : LOG : Protein alignments - 20 seq + 1/12 Test #2: alphabet_utest ................... Passed 0.21 sec + 2/12 Test #3: edist_utest ...................... Passed 0.21 sec + 3/12 Test #4: task_utest ....................... Passed 0.19 sec + 4/12 Test #5: C++Lib ........................... Passed 0.17 sec + 5/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.16 sec + 6/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.11 sec +7: [2024-06-01 09:12:47] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -3211,94 +2488,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec -test 8 - Start 8: kalign_itest_BB12006.msf - -8: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf" -8: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -8: Test timeout computed to be: 1500 -8: -8: Kalign (3.4.0) -8: -8: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -8: -8: This program comes with ABSOLUTELY NO WARRANTY; for details type: -8: `kalign -showw'. -8: This is free software, and you are welcome to redistribute it -8: under certain conditions; consult the COPYING file for details. -8: -8: Please cite: -8: Lassmann, Timo. -8: "Kalign 3: multiple sequence alignment of large data sets." -8: Bioinformatics (2019) -8: https://doi.org/10.1093/bioinformatics/btz795 -8: -8: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -8: [2025-07-04 15:22:42] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -8: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:22:42] : LOG : Building guide tree. -8: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:22:42] : LOG : Aligning -8: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: >1al2_ad -8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS -8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF -8: LFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQ -8: TIDD-----SFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQ -8: KA--- -8: >1bbt_ac -8: GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEACPTFL--R-- -8: ---FEGGVPYVTTKTDSDRV---LAQFDMSLAAK-HMSNTFLAGLAQYYTQYSGTINLHF -8: MFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTGLNSKFTFSIPYLSAADYTY -8: TASDVA--ETTNVQGWVCLFQITH-----GKADGDALVVLASAGKDFELRLPVDARAE-- -8: ----- -8: >1bev_ac -8: G-LPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQV-ESILEAN-N -8: REGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLGTLAKHYTQWSGSVEITC -8: MFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLGTHVIWDFGLQSSITLVIPWISASHFRG -8: VSNDDVLNYQYYAAGHVTIWYQTNMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQ -8: TAILQ -8: >1mec_ac -8: SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI-PTFIGNK-- -8: ---MPNAVPYIEASNTAVKTQ-PLAVYQVTLSCS-CLANTFLAALSRNFAQYRGSLVYTF -8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM -8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP -8: Q---- - 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.01 sec -test 9 - Start 9: kalign_itest_BB12006.tfa - -9: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" -9: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -9: Test timeout computed to be: 1500 -9: -9: Kalign (3.4.0) -9: -9: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -9: -9: This program comes with ABSOLUTELY NO WARRANTY; for details type: -9: `kalign -showw'. -9: This is free software, and you are welcome to redistribute it -9: under certain conditions; consult the COPYING file for details. -9: -9: Please cite: -9: Lassmann, Timo. -9: "Kalign 3: multiple sequence alignment of large data sets." -9: Bioinformatics (2019) -9: https://doi.org/10.1093/bioinformatics/btz795 -9: -9: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -9: [2025-07-04 15:22:42] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -9: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:22:42] : LOG : Building guide tree. -9: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:22:42] : LOG : Aligning -9: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2024-06-01 09:12:47] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3323,38 +2513,7 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- - 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.01 sec -test 10 - Start 10: kalign_itest_BB30014.msf - -10: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa" -10: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -10: Test timeout computed to be: 1500 -10: -10: Kalign (3.4.0) -10: -10: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -10: -10: This program comes with ABSOLUTELY NO WARRANTY; for details type: -10: `kalign -showw'. -10: This is free software, and you are welcome to redistribute it -10: under certain conditions; consult the COPYING file for details. -10: -10: Please cite: -10: Lassmann, Timo. -10: "Kalign 3: multiple sequence alignment of large data sets." -10: Bioinformatics (2019) -10: https://doi.org/10.1093/bioinformatics/btz795 -10: -10: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -10: [2025-07-04 15:22:42] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -10: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:22:42] : LOG : Building guide tree. -10: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:22:42] : LOG : Aligning -10: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:12:47] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -3379,38 +2538,20 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- -10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.01 sec -test 11 - Start 11: kalign_itest_BB30014.tfa - -11: Test command: /build/reproducible-path/kalign-3.4.0/obj-avx2/src/kalign "/build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa" -11: Working Directory: /build/reproducible-path/kalign-3.4.0/tests -11: Test timeout computed to be: 1500 -11: -11: Kalign (3.4.0) -11: -11: Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann -11: -11: This program comes with ABSOLUTELY NO WARRANTY; for details type: -11: `kalign -showw'. -11: This is free software, and you are welcome to redistribute it -11: under certain conditions; consult the COPYING file for details. -11: -11: Please cite: -11: Lassmann, Timo. -11: "Kalign 3: multiple sequence alignment of large data sets." -11: Bioinformatics (2019) -11: https://doi.org/10.1093/bioinformatics/btz795 -11: -11: [2025-07-04 15:22:42] : LOG : Detected protein sequences. -11: [2025-07-04 15:22:42] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-07-04 15:22:42] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-07-04 15:22:42] : LOG : Calculating pairwise distances -11: [2025-07-04 15:22:50] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:08.00 -11: [2025-07-04 15:22:50] : LOG : Building guide tree. -11: [2025-07-04 15:22:50] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-07-04 15:22:50] : LOG : Aligning -11: [2025-07-04 15:22:50] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:00.00 + 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.14 sec + 8/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.11 sec + 9/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.09 sec +11: [2024-06-01 09:12:47] : LOG : CPU Time: 0.06u 00:00:00.05 Elapsed: 00:00:00.00 +11: [2024-06-01 09:12:47] : LOG : Building guide tree. +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: +1: [2024-06-01 09:12:47] : LOG : Testing correctness of AVX bpm. +11: [2024-06-01 09:12:47] : LOG : CPU Time: 0.10u 00:00:00.10 Elapsed: 00:00:00.00 +11: [2024-06-01 09:12:47] : LOG : Aligning +11: [2024-06-01 09:12:47] : LOG : CPU Time: 0.09u 00:00:00.08 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -3719,31 +2860,45 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 7.32 sec -test 12 - Start 12: DSSIM_takes_a_min - -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: [2025-07-04 15:22:50] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-07-04 15:22:50] : LOG : Protein alignments - 20 seq +10/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.34 sec +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: 0 0 0 0 +1: +1: Dyn AVX DYN/AVX +1: [2024-06-01 09:12:59] : LOG : Timing DYN 256 +1: [2024-06-01 09:13:03] : LOG : 2.300992 - dyn +1: [2024-06-01 09:13:03] : LOG : 0.000000 - bpm +1: [2024-06-01 09:13:03] : LOG : 0.191783 - bpm_block2 +1: [2024-06-01 09:13:03] : LOG : 0.184498 - bpm_block +11/12 Test #1: bpm_utest ........................ Passed 16.71 sec 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% [===== ] 10% [===== ] 10% [===== ] 10% [===== ] 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:23:11] : LOG : Protein alignments - 1000 seq +12: [2024-06-01 09:13:57] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:24:03] : LOG : Protein alignments - 10000 seq +12: [2024-06-01 09:14:51] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-07-04 15:24:17] : LOG : DNA alignments - 20 seq +12: [2024-06-01 09:15:27] : 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% [==== ] 8% [==== ] 8% [==== ] 8% [==== ] 9% 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[==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 99% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:25:56] : LOG : DNA alignments - 1000 seq +12: [2024-06-01 09:16:36] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:26:06] : LOG : DNA alignments - 10000 seq +12: [2024-06-01 09:17:20] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 204.41 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 301.26 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 223.30 sec +Total Test time (real) = 301.50 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' +set -e ; for SIMD in avx2 avx sse4.1 ; do \ + if lscpu | grep -q ${SIMD} ; then \ + cd "obj-${SIMD}/" && \ + ctest --verbose ; \ + cd .. ; \ + fi ; \ +done 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 @@ -3762,25 +2917,25 @@ 1: Working Directory: /build/reproducible-path/kalign-3.4.0/obj-avx/lib 1: Test timeout computed to be: 1500 1: LEN: 256 -1: [2025-07-04 15:26:20] : LOG : Testing correctness of serial bpm. +1: [2024-06-01 09:17:53] : 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: [2025-07-04 15:26:20] : LOG : Testing correctness of AVX bpm. +1: [2024-06-01 09:17:53] : 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: [2025-07-04 15:26:28] : LOG : Timing DYN 256 -1: [2025-07-04 15:26:30] : LOG : 2.166680 - dyn -1: [2025-07-04 15:26:30] : LOG : 0.000000 - bpm -1: [2025-07-04 15:26:30] : LOG : 0.147108 - bpm_block2 -1: [2025-07-04 15:26:30] : LOG : 0.146130 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 10.21 sec +1: [2024-06-01 09:18:15] : LOG : Timing DYN 256 +1: [2024-06-01 09:18:24] : LOG : 2.394906 - dyn +1: [2024-06-01 09:18:24] : LOG : 0.000000 - bpm +1: [2024-06-01 09:18:24] : LOG : 0.191081 - bpm_block2 +1: [2024-06-01 09:18:24] : LOG : 0.183615 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 31.31 sec test 2 Start 2: alphabet_utest @@ -3919,78 +3074,78 @@ 2: ] -1 2: ^ -1 2: _ -1 - 2/12 Test #2: alphabet_utest ................... Passed 0.02 sec + 2/12 Test #2: alphabet_utest ................... Passed 0.03 sec test 3 Start 3: edist_utest 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: [2025-07-04 15:26:30] : LOG : Check for correctness. -3: [2025-07-04 15:26:30] : LOG : Timing serial -3: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 - 3/12 Test #3: edist_utest ...................... Passed 0.02 sec +3: [2024-06-01 09:18:24] : LOG : Check for correctness. +3: [2024-06-01 09:18:24] : LOG : Timing serial +3: [2024-06-01 09:18:24] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 + 3/12 Test #3: edist_utest ...................... Passed 0.05 sec test 4 Start 4: task_utest 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: 899 117 245 634 166 -4: 301 846 454 450 56 -4: 254 433 434 619 464 -4: 54 84 300 130 770 -4: 233 507 2 960 295 -4: 718 675 971 181 714 -4: 855 48 639 32 700 -4: 67 291 655 144 715 -4: 632 169 710 805 317 -4: 83 784 312 660 192 -4: 846 804 66 67 581 -4: 861 829 534 313 781 -4: 44 517 191 877 238 -4: 211 961 319 6 540 -4: 505 839 801 182 529 -4: 30 549 227 567 970 -4: 130 162 92 320 723 -4: 275 539 867 399 64 -4: 976 322 426 667 269 -4: 758 985 741 195 556 -4: 827 608 910 337 668 -4: 745 202 723 620 310 -4: 60 671 194 162 73 -4: 951 430 847 520 133 -4: 814 911 890 827 256 -4: 949 115 366 297 197 -4: 16 709 458 112 535 -4: 508 819 676 438 355 -4: 760 553 697 687 329 -4: 135 765 859 131 820 -4: 594 912 767 651 496 -4: 50 521 941 536 444 -4: 273 892 811 840 431 -4: 860 884 3 340 723 -4: 997 341 449 785 751 -4: 428 281 537 768 262 -4: 459 673 300 185 141 -4: 355 158 520 528 787 -4: 982 5 82 60 746 -4: 456 116 74 519 103 -4: 942 560 210 102 12 -4: 644 659 429 456 184 -4: 314 4 958 154 431 -4: 450 285 48 440 850 -4: 351 442 761 230 846 -4: 131 613 783 94 382 -4: 402 185 771 490 24 -4: 598 603 978 970 897 -4: 579 324 237 165 703 -4: 909 483 971 277 290 -4: 148 571 775 811 672 -4: 674 332 192 142 500 -4: 637 146 698 712 128 -4: 442 75 645 859 361 - 4/12 Test #4: task_utest ....................... Passed 0.01 sec +4: 409 908 489 216 54 +4: 408 875 699 650 692 +4: 623 592 149 518 812 +4: 20 553 823 884 51 +4: 61 90 466 553 203 +4: 427 976 385 967 386 +4: 486 137 54 529 331 +4: 318 987 632 245 745 +4: 973 572 931 652 592 +4: 256 508 281 470 905 +4: 745 765 72 685 396 +4: 385 819 991 436 655 +4: 362 395 410 522 329 +4: 807 669 792 876 898 +4: 33 591 259 540 407 +4: 351 78 522 747 206 +4: 199 453 202 827 523 +4: 202 296 807 671 335 +4: 424 944 44 464 254 +4: 22 430 498 909 277 +4: 515 377 718 891 964 +4: 394 557 154 354 915 +4: 371 917 386 978 708 +4: 326 433 985 789 48 +4: 175 34 415 141 301 +4: 153 680 211 832 863 +4: 819 888 924 480 428 +4: 946 546 687 716 936 +4: 70 454 199 136 812 +4: 968 487 408 561 737 +4: 672 129 534 506 476 +4: 210 554 657 983 101 +4: 286 495 941 862 911 +4: 377 769 633 867 289 +4: 735 212 902 537 715 +4: 724 815 210 448 26 +4: 316 59 960 397 208 +4: 185 618 427 979 269 +4: 683 342 615 389 59 +4: 170 538 708 596 161 +4: 631 22 589 842 461 +4: 203 118 649 42 351 +4: 494 515 980 739 801 +4: 362 324 567 114 797 +4: 859 938 982 692 871 +4: 847 83 130 124 488 +4: 515 460 696 531 173 +4: 184 149 970 159 471 +4: 700 801 701 333 352 +4: 948 130 173 267 823 +4: 114 952 693 463 543 +4: 416 255 685 770 629 +4: 602 614 963 794 565 +4: 605 324 769 672 224 + 4/12 Test #4: task_utest ....................... Passed 0.02 sec test 5 Start 5: C++Lib @@ -4002,7 +3157,7 @@ 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 5/12 Test #5: C++Lib ........................... Passed 0.02 sec + 5/12 Test #5: C++Lib ........................... Passed 0.11 sec test 6 Start 6: kalign_itest_BB11001.tfa @@ -4025,15 +3180,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -6: [2025-07-04 15:26:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -6: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:26:30] : LOG : Building guide tree. -6: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:26:30] : LOG : Aligning -6: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:18:24] : LOG : Detected protein sequences. +6: [2024-06-01 09:18:24] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2024-06-01 09:18:24] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:18:24] : LOG : Calculating pairwise distances +6: [2024-06-01 09:18:24] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +6: [2024-06-01 09:18:24] : LOG : Building guide tree. +6: [2024-06-01 09:18:24] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +6: [2024-06-01 09:18:24] : LOG : Aligning +6: [2024-06-01 09:18:24] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4046,7 +3201,7 @@ 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.02 sec + 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.11 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf @@ -4069,15 +3224,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -7: [2025-07-04 15:26:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -7: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:26:30] : LOG : Building guide tree. -7: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:26:30] : LOG : Aligning -7: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2024-06-01 09:18:24] : LOG : Detected protein sequences. +7: [2024-06-01 09:18:24] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2024-06-01 09:18:24] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2024-06-01 09:18:24] : LOG : Calculating pairwise distances +7: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:01.00 +7: [2024-06-01 09:18:25] : LOG : Building guide tree. +7: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +7: [2024-06-01 09:18:25] : LOG : Aligning +7: [2024-06-01 09:18:25] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4090,7 +3245,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.01 sec + 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.10 sec test 8 Start 8: kalign_itest_BB12006.msf @@ -4113,15 +3268,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -8: [2025-07-04 15:26:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -8: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:26:30] : LOG : Building guide tree. -8: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -8: [2025-07-04 15:26:30] : LOG : Aligning -8: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2024-06-01 09:18:25] : LOG : Detected protein sequences. +8: [2024-06-01 09:18:25] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2024-06-01 09:18:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:18:25] : LOG : Calculating pairwise distances +8: [2024-06-01 09:18:25] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:18:25] : LOG : Building guide tree. +8: [2024-06-01 09:18:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:18:25] : LOG : Aligning +8: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4146,7 +3301,7 @@ 8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 8: Q---- - 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.03 sec + 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.06 sec test 9 Start 9: kalign_itest_BB12006.tfa @@ -4169,15 +3324,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -9: [2025-07-04 15:26:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -9: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:26:30] : LOG : Building guide tree. -9: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:26:30] : LOG : Aligning -9: [2025-07-04 15:26:30] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2024-06-01 09:18:25] : LOG : Detected protein sequences. +9: [2024-06-01 09:18:25] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2024-06-01 09:18:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2024-06-01 09:18:25] : LOG : Calculating pairwise distances +9: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2024-06-01 09:18:25] : LOG : Building guide tree. +9: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 +9: [2024-06-01 09:18:25] : LOG : Aligning +9: [2024-06-01 09:18:25] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4202,7 +3357,7 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- - 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.02 sec + 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.09 sec test 10 Start 10: kalign_itest_BB30014.msf @@ -4225,15 +3380,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -10: [2025-07-04 15:26:30] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -10: [2025-07-04 15:26:30] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:26:30] : LOG : Building guide tree. -10: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:26:30] : LOG : Aligning -10: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:18:25] : LOG : Detected protein sequences. +10: [2024-06-01 09:18:25] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2024-06-01 09:18:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:18:25] : LOG : Calculating pairwise distances +10: [2024-06-01 09:18:25] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +10: [2024-06-01 09:18:25] : LOG : Building guide tree. +10: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +10: [2024-06-01 09:18:25] : LOG : Aligning +10: [2024-06-01 09:18:25] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -4258,7 +3413,7 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- -10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.02 sec +10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.10 sec test 11 Start 11: kalign_itest_BB30014.tfa @@ -4281,15 +3436,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-07-04 15:26:30] : LOG : Detected protein sequences. -11: [2025-07-04 15:26:30] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-07-04 15:26:30] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-07-04 15:26:30] : LOG : Calculating pairwise distances -11: [2025-07-04 15:26:30] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-07-04 15:26:30] : LOG : Building guide tree. -11: [2025-07-04 15:26:31] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:01.00 -11: [2025-07-04 15:26:31] : LOG : Aligning -11: [2025-07-04 15:26:31] : LOG : CPU Time: 0.06u 00:00:00.05 Elapsed: 00:00:00.00 +11: [2024-06-01 09:18:25] : LOG : Detected protein sequences. +11: [2024-06-01 09:18:25] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2024-06-01 09:18:25] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2024-06-01 09:18:25] : LOG : Calculating pairwise distances +11: [2024-06-01 09:18:25] : LOG : CPU Time: 0.05u 00:00:00.04 Elapsed: 00:00:00.00 +11: [2024-06-01 09:18:25] : LOG : Building guide tree. +11: [2024-06-01 09:18:25] : LOG : CPU Time: 0.09u 00:00:00.08 Elapsed: 00:00:00.00 +11: [2024-06-01 09:18:25] : LOG : Aligning +11: [2024-06-01 09:18:25] : LOG : CPU Time: 0.08u 00:00:00.08 Elapsed: 00:00:00.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -4598,31 +3753,31 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.12 sec +11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.29 sec test 12 Start 12: DSSIM_takes_a_min 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: [2025-07-04 15:26:31] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-07-04 15:26:31] : LOG : Protein alignments - 20 seq +12: [2024-06-01 09:18:25] : LOG : DSSim - a simplistic sequence simulator. +12: [2024-06-01 09:18:25] : 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% [=== 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09:20:03] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:27:22] : LOG : Protein alignments - 10000 seq +12: [2024-06-01 09:20:52] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-07-04 15:27:40] : LOG : DNA alignments - 20 seq +12: [2024-06-01 09:21:29] : 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% 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:28:11] : LOG : DNA alignments - 1000 seq +12: [2024-06-01 09:22:36] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:28:21] : LOG : DNA alignments - 10000 seq +12: [2024-06-01 09:23:06] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 129.41 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 300.92 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 139.92 sec +Total Test time (real) = 333.20 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 @@ -4641,25 +3796,25 @@ 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: [2025-07-04 15:28:40] : LOG : Testing correctness of serial bpm. +1: [2024-06-01 09:23:26] : 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: [2025-07-04 15:28:40] : LOG : Testing correctness of AVX bpm. +1: [2024-06-01 09:23:27] : 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: [2025-07-04 15:28:48] : LOG : Timing DYN 256 -1: [2025-07-04 15:28:51] : LOG : 2.141624 - dyn -1: [2025-07-04 15:28:51] : LOG : 0.000000 - bpm -1: [2025-07-04 15:28:51] : LOG : 0.143510 - bpm_block2 -1: [2025-07-04 15:28:51] : LOG : 0.147364 - bpm_block - 1/12 Test #1: bpm_utest ........................ Passed 10.88 sec +1: [2024-06-01 09:23:38] : LOG : Timing DYN 256 +1: [2024-06-01 09:23:43] : LOG : 2.465999 - dyn +1: [2024-06-01 09:23:43] : LOG : 0.000000 - bpm +1: [2024-06-01 09:23:43] : LOG : 0.195577 - bpm_block2 +1: [2024-06-01 09:23:43] : LOG : 0.192291 - bpm_block + 1/12 Test #1: bpm_utest ........................ Passed 16.60 sec test 2 Start 2: alphabet_utest @@ -4798,77 +3953,77 @@ 2: ] -1 2: ^ -1 2: _ -1 - 2/12 Test #2: alphabet_utest ................... Passed 0.01 sec + 2/12 Test #2: alphabet_utest ................... Passed 0.02 sec test 3 Start 3: edist_utest 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: [2025-07-04 15:28:51] : LOG : Check for correctness. -3: [2025-07-04 15:28:51] : LOG : Timing serial -3: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 - 3/12 Test #3: edist_utest ...................... Passed 0.02 sec +3: [2024-06-01 09:23:43] : LOG : Check for correctness. +3: [2024-06-01 09:23:43] : LOG : Timing serial +3: [2024-06-01 09:23:43] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 + 3/12 Test #3: edist_utest ...................... Passed 0.03 sec test 4 Start 4: task_utest 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: 14 160 803 160 195 -4: 559 373 534 355 517 -4: 962 464 585 687 462 -4: 477 248 139 977 151 -4: 521 324 299 88 215 -4: 86 69 273 168 720 -4: 721 728 687 153 747 -4: 213 978 75 568 822 -4: 297 351 574 11 961 -4: 968 765 936 483 643 -4: 419 524 734 13 980 -4: 906 155 84 938 876 -4: 325 638 263 48 98 -4: 495 110 873 677 607 -4: 585 262 692 106 858 -4: 174 238 866 618 224 -4: 967 83 383 842 303 -4: 806 630 155 796 16 -4: 417 772 143 993 868 -4: 41 112 529 981 93 -4: 958 401 294 711 788 -4: 109 356 600 48 701 -4: 238 431 603 533 860 -4: 67 78 276 322 932 -4: 940 622 544 491 939 -4: 257 448 354 324 520 -4: 446 472 37 35 940 -4: 785 857 369 766 814 -4: 828 658 471 301 383 -4: 803 701 9 698 606 -4: 955 400 490 524 47 -4: 199 49 575 574 533 -4: 684 354 676 446 611 -4: 311 829 796 54 155 -4: 552 423 564 887 443 -4: 781 853 501 923 968 -4: 226 143 85 150 998 -4: 659 882 654 509 303 -4: 495 759 485 792 782 -4: 164 564 663 367 933 -4: 857 815 935 646 471 -4: 277 294 179 5 118 -4: 981 754 284 555 560 -4: 234 914 555 283 938 -4: 108 826 83 888 522 -4: 711 942 343 683 57 -4: 745 173 284 748 645 -4: 492 273 322 341 554 -4: 778 873 813 796 495 -4: 100 153 664 640 233 -4: 575 850 895 113 985 -4: 274 639 291 689 17 -4: 202 190 114 574 833 -4: 320 23 667 400 198 +4: 979 869 965 221 247 +4: 825 40 545 485 775 +4: 700 419 801 410 303 +4: 570 375 420 934 877 +4: 721 386 253 145 795 +4: 102 1 497 683 399 +4: 356 695 542 546 114 +4: 104 583 749 403 826 +4: 96 938 622 523 817 +4: 755 228 566 972 227 +4: 685 876 673 603 144 +4: 968 331 360 337 830 +4: 128 492 864 316 907 +4: 790 989 506 713 502 +4: 547 970 611 799 614 +4: 727 299 974 643 420 +4: 623 763 239 433 374 +4: 431 454 964 869 273 +4: 328 934 677 846 652 +4: 304 405 159 989 826 +4: 896 409 494 426 346 +4: 0 484 690 657 179 +4: 966 834 372 955 566 +4: 584 37 508 966 497 +4: 157 611 713 497 314 +4: 935 528 54 198 297 +4: 582 273 133 732 283 +4: 994 620 348 588 793 +4: 595 959 586 76 295 +4: 495 720 531 137 271 +4: 8 873 31 131 818 +4: 717 418 448 350 333 +4: 725 835 132 56 670 +4: 285 281 453 673 567 +4: 498 285 477 936 301 +4: 448 641 231 877 324 +4: 561 872 284 733 577 +4: 564 33 123 641 432 +4: 371 756 482 375 626 +4: 28 488 567 385 547 +4: 477 436 137 458 74 +4: 456 744 550 264 7 +4: 964 838 194 720 858 +4: 234 293 761 636 446 +4: 483 985 164 766 550 +4: 271 321 574 307 586 +4: 937 363 905 156 319 +4: 144 130 377 477 908 +4: 169 942 597 738 668 +4: 960 350 671 26 149 +4: 858 63 862 736 522 +4: 397 954 256 858 638 +4: 29 237 8 995 266 +4: 330 635 585 316 816 4/12 Test #4: task_utest ....................... Passed 0.01 sec test 5 Start 5: C++Lib @@ -4881,7 +4036,7 @@ 5: ------MQDRVKRPMNAFIVWSRDQRRKMALENPRMR-NS-EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK 5: MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NL-DLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK--- 5: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 5/12 Test #5: C++Lib ........................... Passed 0.02 sec + 5/12 Test #5: C++Lib ........................... Passed 0.08 sec test 6 Start 6: kalign_itest_BB11001.tfa @@ -4904,15 +4059,15 @@ 6: Bioinformatics (2019) 6: https://doi.org/10.1093/bioinformatics/btz795 6: -6: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -6: [2025-07-04 15:28:51] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. -6: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -6: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:28:51] : LOG : Building guide tree. -6: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -6: [2025-07-04 15:28:51] : LOG : Aligning -6: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +6: [2024-06-01 09:23:43] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001.tfa. +6: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +6: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +6: [2024-06-01 09:23:43] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 +6: [2024-06-01 09:23:43] : LOG : Building guide tree. +6: [2024-06-01 09:23:43] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +6: [2024-06-01 09:23:43] : LOG : Aligning +6: [2024-06-01 09:23:43] : LOG : CPU Time: 0.02u 00:00:00.02 Elapsed: 00:00:00.00 6: >1aab_ 6: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 6: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4925,7 +4080,7 @@ 6: >2lef_A 6: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 6: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.03 sec + 6/12 Test #6: kalign_itest_BB11001.tfa ......... Passed 0.08 sec test 7 Start 7: kalign_itest_BB11001_EOF.msf @@ -4948,15 +4103,15 @@ 7: Bioinformatics (2019) 7: https://doi.org/10.1093/bioinformatics/btz795 7: -7: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -7: [2025-07-04 15:28:51] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. -7: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -7: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:28:51] : LOG : Building guide tree. -7: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -7: [2025-07-04 15:28:51] : LOG : Aligning -7: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +7: [2024-06-01 09:23:43] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB11001_EOF.msf. +7: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +7: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +7: [2024-06-01 09:23:43] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +7: [2024-06-01 09:23:43] : LOG : Building guide tree. +7: [2024-06-01 09:23:43] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +7: [2024-06-01 09:23:43] : LOG : Aligning +7: [2024-06-01 09:23:43] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 7: >1aab_ 7: ---GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 7: KFEDMAKADKARYEREMKTYIPPKGE---------- @@ -4969,7 +4124,7 @@ 7: >2lef_A 7: --------MHIKKPLNAFMLYMKEMRANVVAESTLKE-SA-AINQILGRRWHALSREEQA 7: KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK - 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.03 sec + 7/12 Test #7: kalign_itest_BB11001_EOF.msf ..... Passed 0.09 sec test 8 Start 8: kalign_itest_BB12006.msf @@ -4992,15 +4147,15 @@ 8: Bioinformatics (2019) 8: https://doi.org/10.1093/bioinformatics/btz795 8: -8: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -8: [2025-07-04 15:28:51] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. -8: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -8: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -8: [2025-07-04 15:28:51] : LOG : Building guide tree. -8: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 -8: [2025-07-04 15:28:51] : LOG : Aligning -8: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +8: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +8: [2024-06-01 09:23:43] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.msf. +8: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +8: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:23:43] : LOG : Building guide tree. +8: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +8: [2024-06-01 09:23:43] : LOG : Aligning +8: [2024-06-01 09:23:43] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 8: >1al2_ad 8: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 8: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5025,7 +4180,7 @@ 8: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 8: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 8: Q---- - 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.05 sec + 8/12 Test #8: kalign_itest_BB12006.msf ......... Passed 0.06 sec test 9 Start 9: kalign_itest_BB12006.tfa @@ -5048,15 +4203,15 @@ 9: Bioinformatics (2019) 9: https://doi.org/10.1093/bioinformatics/btz795 9: -9: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -9: [2025-07-04 15:28:51] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -9: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -9: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:28:51] : LOG : Building guide tree. -9: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -9: [2025-07-04 15:28:51] : LOG : Aligning -9: [2025-07-04 15:28:51] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +9: [2024-06-01 09:23:43] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +9: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +9: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +9: [2024-06-01 09:23:43] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +9: [2024-06-01 09:23:43] : LOG : Building guide tree. +9: [2024-06-01 09:23:43] : LOG : CPU Time: 0.03u 00:00:00.02 Elapsed: 00:00:00.00 +9: [2024-06-01 09:23:43] : LOG : Aligning +9: [2024-06-01 09:23:43] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 9: >1al2_ad 9: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 9: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5081,7 +4236,7 @@ 9: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 9: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 9: Q---- - 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.03 sec + 9/12 Test #9: kalign_itest_BB12006.tfa ......... Passed 0.07 sec test 10 Start 10: kalign_itest_BB30014.msf @@ -5104,15 +4259,15 @@ 10: Bioinformatics (2019) 10: https://doi.org/10.1093/bioinformatics/btz795 10: -10: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -10: [2025-07-04 15:28:51] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. -10: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -10: [2025-07-04 15:28:51] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:28:51] : LOG : Building guide tree. -10: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -10: [2025-07-04 15:28:51] : LOG : Aligning -10: [2025-07-04 15:28:51] : LOG : CPU Time: 0.02u 00:00:00.01 Elapsed: 00:00:00.00 +10: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +10: [2024-06-01 09:23:43] : LOG : Read 4 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB12006.tfa. +10: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +10: [2024-06-01 09:23:43] : LOG : CPU Time: 0.01u 00:00:00.01 Elapsed: 00:00:00.00 +10: [2024-06-01 09:23:43] : LOG : Building guide tree. +10: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +10: [2024-06-01 09:23:43] : LOG : Aligning +10: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 10: >1al2_ad 10: G-LPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEI-DTMIPFDLS 10: ATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTF @@ -5137,7 +4292,7 @@ 10: VFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRM 10: VGTDQA--NITNVDGWVTVWQLTPLTYPPGCPTSAKILTMVSAGKDFSLKMPISPAPWSP 10: Q---- -10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.03 sec +10/12 Test #10: kalign_itest_BB30014.msf ......... Passed 0.05 sec test 11 Start 11: kalign_itest_BB30014.tfa @@ -5160,15 +4315,15 @@ 11: Bioinformatics (2019) 11: https://doi.org/10.1093/bioinformatics/btz795 11: -11: [2025-07-04 15:28:51] : LOG : Detected protein sequences. -11: [2025-07-04 15:28:51] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. -11: [2025-07-04 15:28:51] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -11: [2025-07-04 15:28:51] : LOG : Calculating pairwise distances -11: [2025-07-04 15:28:51] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 -11: [2025-07-04 15:28:51] : LOG : Building guide tree. -11: [2025-07-04 15:28:51] : LOG : CPU Time: 0.04u 00:00:00.04 Elapsed: 00:00:00.00 -11: [2025-07-04 15:28:51] : LOG : Aligning -11: [2025-07-04 15:28:51] : LOG : CPU Time: 0.05u 00:00:00.05 Elapsed: 00:00:00.00 +11: [2024-06-01 09:23:43] : LOG : Detected protein sequences. +11: [2024-06-01 09:23:43] : LOG : Read 44 sequences from /build/reproducible-path/kalign-3.4.0/tests/data/BB30014.tfa. +11: [2024-06-01 09:23:43] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +11: [2024-06-01 09:23:43] : LOG : Calculating pairwise distances +11: [2024-06-01 09:23:43] : LOG : CPU Time: 0.03u 00:00:00.03 Elapsed: 00:00:00.00 +11: [2024-06-01 09:23:43] : LOG : Building guide tree. +11: [2024-06-01 09:23:43] : LOG : CPU Time: 0.10u 00:00:00.09 Elapsed: 00:00:00.00 +11: [2024-06-01 09:23:43] : LOG : Aligning +11: [2024-06-01 09:23:44] : LOG : CPU Time: 0.08u 00:00:00.08 Elapsed: 00:00:01.00 11: >1ags_A 11: ----------------------------------AEKPKLHYFNARGRMESTRWLLAAAG 11: VEFEEKFIKSAEDLDKLRNDG--YLMFQQVPMVEI-----DG--MKLVQTRAILNYIA-- @@ -5477,36 +4632,36 @@ 11: ----KNPDLREEKFA-DIKKAYDNAEQLLT----GDFYS-GTSKPGFVDYLLYPNIQRAY 11: WAAHIVPDFPLEAESFPGPN-YPRLSKWYKAL-ESIPEVAAASQPTENGVGFFKDYLGGS 11: PNYDYGLTKLSETI -11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.13 sec +11/12 Test #11: kalign_itest_BB30014.tfa ......... Passed 0.21 sec test 12 Start 12: DSSIM_takes_a_min 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: [2025-07-04 15:28:51] : LOG : DSSim - a simplistic sequence simulator. -12: [2025-07-04 15:28:51] : LOG : Protein alignments - 20 seq +12: [2024-06-01 09:23:44] : LOG : DSSim - a simplistic sequence simulator. +12: [2024-06-01 09:23:44] : 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% 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09:24:45] : LOG : Protein alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:29:53] : LOG : Protein alignments - 10000 seq +12: [2024-06-01 09:25:26] : LOG : Protein alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12: [2025-07-04 15:30:07] : LOG : DNA alignments - 20 seq +12: [2024-06-01 09:25:59] : 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% 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[==================================================] 100% [==================================================] 100% [==================================================] 100% [==================================================] 100% -12: [2025-07-04 15:30:33] : LOG : DNA alignments - 1000 seq +12: [2024-06-01 09:27:09] : LOG : DNA alignments - 1000 seq 12: [ ] 0% [===== ] 10% [========== ] 20% [=============== ] 30% [==================== ] 40% [========================= ] 50% [============================== ] 60% [=================================== ] 70% [======================================== ] 80% [============================================= ] 90% [==================================================] 100% -12: [2025-07-04 15:30:45] : LOG : DNA alignments - 10000 seq +12: [2024-06-01 09:27:39] : LOG : DNA alignments - 10000 seq 12: [ ] 0% [========================= ] 50% [==================================================] 100% -12/12 Test #12: DSSIM_takes_a_min ................ Passed 124.90 sec +12/12 Test #12: DSSIM_takes_a_min ................ Passed 255.16 sec 100% tests passed, 0 tests failed out of 12 -Total Test time (real) = 136.19 sec +Total Test time (real) = 272.49 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 -j42 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 -j20 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 @@ -5565,8 +4720,8 @@ make[1]: Leaving directory '/build/reproducible-path/kalign-3.4.0' dh_md5sums dh_builddeb -dpkg-deb: building package 'kalign' in '../kalign_3.4.0-1_amd64.deb'. dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.4.0-1_amd64.deb'. +dpkg-deb: building package 'kalign' in '../kalign_3.4.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../kalign_3.4.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../kalign_3.4.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5574,12 +4729,14 @@ 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/3073256/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3073256/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/119659 and its subdirectories -I: Current time: Fri Jul 4 03:32:11 -12 2025 -I: pbuilder-time-stamp: 1751643131 +I: removing directory /srv/workspace/pbuilder/3073256 and its subdirectories +I: Current time: Sat Jun 1 23:28:27 +14 2024 +I: pbuilder-time-stamp: 1717234107