Diff of the two buildlogs: -- --- b1/build.log 2025-09-10 05:55:37.450860150 +0000 +++ b2/build.log 2025-09-10 06:05:04.575609035 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 13 00:06:08 -12 2026 -I: pbuilder-time-stamp: 1791893168 +I: Current time: Wed Sep 10 19:55:39 +14 2025 +I: pbuilder-time-stamp: 1757483739 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -31,53 +31,85 @@ dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3607408/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3897769/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 Sep 10 05:55 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3897769/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3897769/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='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='07df5a6fd7704e1e9281f0127eb31176' - 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='3607408' - PS1='# ' - PS2='> ' + INVOCATION_ID=6dc3b9a7c57445febca4d5f211105406 + 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=3897769 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.NMMeiD92/pbuilderrc_znnW --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NMMeiD92/b1 --logfile b1/build.log hhsuite_3.3.0+ds-8.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - 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.NMMeiD92/pbuilderrc_53BN --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.NMMeiD92/b2 --logfile b2/build.log hhsuite_3.3.0+ds-8.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + 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 ionos5-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3607408/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3897769/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -222,7 +254,7 @@ Get: 99 http://deb.debian.org/debian forky/main amd64 imagemagick-7.q16 amd64 8:7.1.2.3+dfsg1-1 [728 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 imagemagick amd64 8:7.1.2.3+dfsg1-1 [21.6 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libsimde-dev all 0.8.2-3 [467 kB] -Fetched 45.8 MB in 12s (3871 kB/s) +Fetched 45.8 MB in 5s (9327 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) @@ -672,7 +704,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes +I: user script /srv/workspace/pbuilder/3897769/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3897769/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hhsuite-3.3.0+ds/ && 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 > ../hhsuite_3.3.0+ds-8_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-8 dpkg-buildpackage: info: source distribution unstable @@ -742,8 +778,8 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (9.1s) --- Generating done (0.2s) +-- Configuring done (2.0s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -799,7 +835,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (5.4s) +-- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -856,7 +892,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (9.0s) +-- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -913,8 +949,8 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (6.5s) --- Generating done (0.4s) +-- Configuring done (1.9s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -970,7 +1006,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (9.6s) +-- Configuring done (1.8s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1029,8 +1065,8 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (8.6s) --- Generating done (0.3s) +-- Configuring done (1.8s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1090,7 +1126,7 @@ -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP --- Configuring done (7.3s) +-- Configuring done (1.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -1111,7 +1147,7 @@ for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_build --builddirectory build_${SIMD} ; \ done - cd build_avx2 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_avx2 && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2//CMakeFiles/progress.marks @@ -1140,18 +1176,18 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build -make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build +make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' @@ -1159,49 +1195,46 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 1%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -[ 3%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -[ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -[ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -[ 7%] Generating ../generated/context_data.lib.h -[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -[ 7%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -[ 7%] Generating ../generated/cs219.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +[ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 5%] Generating ../generated/context_data.crf.h +[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +[ 5%] Generating ../generated/context_data.lib.h +[ 6%] Generating ../generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/cs219.lib.h [ 16%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 -/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o -/usr/bin/ranlib libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); @@ -1217,6 +1250,9 @@ /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ +/usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o +/usr/bin/ranlib libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' [ 16%] Built target ffindex make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend @@ -1227,9 +1263,9 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend @@ -1248,52 +1284,48 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 17%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c +[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o +[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde 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CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); @@ -1301,62 +1333,65 @@ | | | | long long int int64_t {aka long int} | %ld +[ 26%] Linking C executable ffindex_get +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 +[ 27%] Linking C executable ffindex_reduce +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 +[ 28%] Linking C executable ffindex_modify +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 +[ 29%] Linking C executable ffindex_unpack +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 +[ 30%] Linking C executable ffindex_from_fasta_with_split +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_get.dir/link.d CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 30%] Linking C executable ffindex_order -[ 29%] Linking C executable ffindex_modify -[ 30%] Built target ffindex_get -[ 30%] Linking C executable ffindex_reduce -[ 30%] Built target ffindex_unpack -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 +[ 31%] Linking C executable ffindex_order cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 -[ 31%] Linking C executable ffindex_from_fasta +[ 31%] Built target ffindex_get +[ 31%] Built target ffindex_reduce +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a +[ 32%] Linking C executable ffindex_from_fasta +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 -[ 32%] Linking C executable ffindex_from_fasta_with_split -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a +[ 32%] Built target ffindex_modify make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 33%] Built target ffindex_order -[ 33%] Linking C executable ffindex_build -[ 33%] Built target ffindex_reduce -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 -[ 33%] Built target ffindex_modify +[ 33%] Linking C executable ffindex_apply +[ 33%] Built target ffindex_from_fasta_with_split +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 +[ 33%] Built target ffindex_unpack /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a +[ 34%] Linking C executable ffindex_build +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a -[ 34%] Linking C executable ffindex_apply +[ 34%] Built target ffindex_order [ 34%] Built target ffindex_from_fasta -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 34%] Built target ffindex_from_fasta_with_split -[ 34%] Built target ffindex_build -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' [ 34%] Built target ffindex_apply +[ 34%] Built target ffindex_build [ 35%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp [ 35%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/depend make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/depend make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/depend -make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/depend -make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_extract-avx2.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/depend +make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/a3m_reduce-avx2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' @@ -1368,150 +1403,151 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/build make -f src/CMakeFiles/a3m_extract-avx2.dir/build.make src/CMakeFiles/a3m_extract-avx2.dir/build make -f src/CMakeFiles/a3m_reduce-avx2.dir/build.make src/CMakeFiles/a3m_reduce-avx2.dir/build -make -f src/CMakeFiles/a3m_database_reduce-avx2.dir/build.make src/CMakeFiles/a3m_database_reduce-avx2.dir/build -make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/build +make -f src/CMakeFiles/a3m_database_filter-avx2.dir/build.make src/CMakeFiles/a3m_database_filter-avx2.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make -f src/CMakeFiles/a3m_database_extract-avx2.dir/build.make src/CMakeFiles/a3m_database_extract-avx2.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h +[ 39%] Building CXX object src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o +[ 39%] Building CXX object src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o +[ 39%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o [ 40%] Building CXX object src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -[ 38%] Building CXX object src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -[ 40%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o [ 40%] Building CXX object src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -[ 40%] Building CXX object src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -[ 41%] Linking CXX static library libhhviterbialgorithm_and_ss.a +[ 41%] Linking CXX static library libCS_OBJECTS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 +/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o +/usr/bin/ranlib libCS_OBJECTS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 41%] Built target CS_OBJECTS +[ 42%] Linking CXX executable a3m_extract-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx2.dir/link.txt --verbose=1 +[ 43%] Linking CXX executable a3m_reduce-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx2.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp +[ 44%] Linking CXX executable a3m_database_reduce-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx2.dir/link.txt --verbose=1 +[ 45%] Linking CXX executable a3m_database_extract-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-avx2.dir/link.d "CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o" -o a3m_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 46%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -[ 42%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +[ 47%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx2.dir/link.d "CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 47%] Built target a3m_extract-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -[ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -[ 43%] Built target hhviterbialgorithm_and_ss +[ 47%] Built target a3m_reduce-avx2 +[ 48%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 43%] Built target hhviterbialgorithm_with_celloff -/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 44%] Linking CXX executable a3m_reduce-avx2 -[ 45%] Linking CXX executable a3m_extract-avx2 -[ 45%] Built target hhviterbialgorithm_with_celloff_and_ss -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx2.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx2.dir/link.txt --verbose=1 -[ 46%] Linking CXX static library libCS_OBJECTS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 -[ 48%] Linking CXX executable a3m_database_reduce-avx2 -[ 48%] Linking CXX executable a3m_database_extract-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx2.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx2.dir/link.txt --verbose=1 -/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o -/usr/bin/ranlib libCS_OBJECTS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx2.dir/link.d "CMakeFiles/a3m_reduce-avx2.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-avx2.dir/link.d "CMakeFiles/a3m_extract-avx2.dir/a3m_extract.cpp.o" -o a3m_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-avx2.dir/link.d "CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a +[ 48%] Built target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 48%] Built target CS_OBJECTS -[ 48%] Built target a3m_reduce-avx2 -[ 48%] Built target a3m_extract-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-avx2.dir/link.d "CMakeFiles/a3m_database_reduce-avx2.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-avx2.dir/link.d "CMakeFiles/a3m_database_extract-avx2.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +[ 48%] Built target a3m_database_reduce-avx2 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.lib.h +/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a +[ 48%] Built target hhviterbialgorithm_and_ss make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 48%] Built target generated -[ 48%] Built target a3m_database_reduce-avx2 [ 48%] Built target a3m_database_extract-avx2 +[ 48%] Built target hhviterbialgorithm_with_celloff_and_ss +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp +[ 49%] Linking CXX executable a3m_database_filter-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-avx2.dir/link.d "CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 49%] Built target a3m_database_filter-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated/context_data.crf.h +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 49%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake "--color=" -[ 49%] Linking CXX executable a3m_database_filter-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-avx2.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o +[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp +[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/util.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp +[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o +[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp +[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhutil.cpp +[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp +[ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o 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src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp +[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp +[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp +[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp +[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp -[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp -[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp [ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp -[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-avx2.dir/link.d "CMakeFiles/a3m_database_filter-avx2.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx2 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 78%] Built target a3m_database_filter-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -1548,90 +1584,90 @@ make -f src/CMakeFiles/hhmake-avx2.dir/build.make src/CMakeFiles/hhmake-avx2.dir/depend make -f src/CMakeFiles/hhfilter-avx2.dir/build.make src/CMakeFiles/hhfilter-avx2.dir/depend make -f src/CMakeFiles/hhsearch-avx2.dir/build.make src/CMakeFiles/hhsearch-avx2.dir/depend -make -f src/CMakeFiles/hhalign-avx2.dir/build.make src/CMakeFiles/hhalign-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits-avx2.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/hhalign-avx2.dir/build.make src/CMakeFiles/hhalign-avx2.dir/depend +make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhmake-avx2.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhconsensus-avx2.dir/build.make src/CMakeFiles/hhconsensus-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhfilter-avx2.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/cstranslate-avx2.dir/build.make src/CMakeFiles/cstranslate-avx2.dir/depend +make -f src/CMakeFiles/hhblits_omp-avx2.dir/build.make src/CMakeFiles/hhblits_omp-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhsearch-avx2.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_omp-avx2.dir/build.make src/CMakeFiles/hhblits_omp-avx2.dir/depend +make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhalign-avx2.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhsearch_omp-avx2.dir/build.make src/CMakeFiles/hhsearch_omp-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhconsensus-avx2.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhalign_omp-avx2.dir/build.make src/CMakeFiles/hhalign_omp-avx2.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src 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cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhsearch_omp-avx2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_ca3m-avx2.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhalign_omp-avx2.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_omp-avx2.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src/CMakeFiles/hhblits_ca3m-avx2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' make -f src/CMakeFiles/hhblits-avx2.dir/build.make src/CMakeFiles/hhblits-avx2.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make[4]: Leaving 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CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp +[ 90%] Building CXX object src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1659,8 +1695,10 @@ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable hhblits-avx2 -[ 92%] Linking CXX executable hhalign-avx2 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx2.dir/link.txt --verbose=1 +[ 92%] Linking CXX executable hhsearch-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx2.dir/link.txt --verbose=1 +[ 93%] Linking CXX executable hhalign-avx2 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx2.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] @@ -1716,40 +1754,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhblits_ca3m-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-avx2.dir/link.d "CMakeFiles/hhblits-avx2.dir/hhblits_app.cpp.o" -o hhblits-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 94%] Linking CXX executable hhsearch-avx2 +[ 94%] Linking CXX executable hhblits_ca3m-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx2.dir/link.txt --verbose=1 [ 94%] Built target hhblits-avx2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx2.dir/link.d "CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o" -o hhalign-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx2.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 94%] Built target hhalign-avx2 -[ 95%] Linking CXX executable hhalign_omp-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx2.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable hhblits_omp-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-avx2.dir/link.d "CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 97%] Linking CXX executable hhfilter-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx2.dir/link.txt --verbose=1 -[ 97%] Built target hhblits_ca3m-avx2 -[ 98%] Linking CXX executable hhmake-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx2.dir/link.d "CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-avx2.dir/link.d "CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o" -o hhsearch-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 98%] Built target hhalign_omp-avx2 -[ 98%] Built target hhsearch-avx2 -[ 99%] Linking CXX executable hhconsensus-avx2 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-avx2.dir/link.d "CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o" -o hhfilter-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 99%] Built target hhfilter-avx2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx2.dir/link.d "CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -1777,18 +1786,45 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 99%] Built target hhblits_omp-avx2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-avx2.dir/link.d "CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o" -o hhmake-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 95%] Linking CXX executable hhblits_omp-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx2.dir/link.d "CMakeFiles/hhalign-avx2.dir/hhblits_app.cpp.o" -o hhalign-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[ 99%] Built target hhmake-avx2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx2.dir/link.d "CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o" -o hhconsensus-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-avx2.dir/link.d "CMakeFiles/hhsearch-avx2.dir/hhblits_app.cpp.o" -o hhsearch-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' -[100%] Linking CXX executable hhsearch_omp-avx2 -[100%] Built target hhconsensus-avx2 +[ 96%] Linking CXX executable hhalign_omp-avx2 +[ 96%] Built target hhalign-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx2.dir/link.txt --verbose=1 +[ 96%] Built target hhsearch-avx2 +[ 97%] Linking CXX executable hhsearch_omp-avx2 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-avx2.dir/link.d "CMakeFiles/hhblits_ca3m-avx2.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx2.dir/link.d "CMakeFiles/hhblits_omp-avx2.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 97%] Built target hhblits_ca3m-avx2 +[ 97%] Built target hhblits_omp-avx2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx2.dir/link.d "CMakeFiles/hhalign_omp-avx2.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[ 97%] Built target hhalign_omp-avx2 +[ 98%] Linking CXX executable hhfilter-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx2.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable hhconsensus-avx2 +[100%] Linking CXX executable hhmake-avx2 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx2.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-avx2.dir/link.d "CMakeFiles/hhsearch_omp-avx2.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' [100%] Built target hhsearch_omp-avx2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-avx2.dir/link.d "CMakeFiles/hhfilter-avx2.dir/hhfilter.cpp.o" -o hhfilter-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[100%] Built target hhfilter-avx2 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-avx2.dir/link.d "CMakeFiles/hhmake-avx2.dir/hhmake.cpp.o" -o hhmake-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx2.dir/link.d "CMakeFiles/hhconsensus-avx2.dir/hhconsensus.cpp.o" -o hhconsensus-avx2 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' +[100%] Built target hhmake-avx2 +[100%] Built target hhconsensus-avx2 [100%] Linking CXX executable cstranslate-avx2 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-avx2.dir/link.d "CMakeFiles/cstranslate-avx2.dir/cs/cstranslate_app.cc.o" -o cstranslate-avx2 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -1797,7 +1833,7 @@ make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_avx2/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' - cd build_avx && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_avx && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_avx//CMakeFiles/progress.marks @@ -1828,60 +1864,63 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build -make -f 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lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 6%] Generating ../generated/context_data.lib.h +[ 6%] Generating ../generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/cs219.lib.h +[ 16%] Linking C static library libffindex.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp:504:43: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 504 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); @@ -1897,9 +1936,6 @@ /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ -[ 16%] Linking C static library libffindex.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' @@ -1910,12 +1946,12 @@ make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" @@ -1932,50 +1968,50 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 17%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c -[ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o +[ 17%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o +[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c +[ 19%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o +[ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -UHAVE_MPI -MD -MT 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ffindex_modify libffindex.a +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 33%] Built target ffindex_get +[ 33%] Built target ffindex_modify +[ 33%] Built target ffindex_reduce +[ 33%] Built target ffindex_from_fasta +[ 33%] Built target ffindex_from_fasta_with_split +[ 33%] Built target ffindex_unpack +[ 33%] Built target ffindex_order +[ 33%] Built target ffindex_apply +[ 34%] Linking C executable ffindex_build +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 34%] Built target ffindex_build +[ 35%] Linking CXX static library libA3M_COMPRESS.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P 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libA3M_COMPRESS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 -[ 35%] Linking C executable ffindex_reduce -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 [ 35%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/depend make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/depend @@ -2016,168 +2079,145 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_extract-avx.dir/DependInfo.cmake "--color=" make -f 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CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/build -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_get.dir/link.d CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta.dir/link.d CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a -make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/a3m_database_filter-avx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_extract-avx.dir/build.make src/CMakeFiles/a3m_extract-avx.dir/build +make -f src/CMakeFiles/a3m_database_extract-avx.dir/build.make src/CMakeFiles/a3m_database_extract-avx.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/a3m_database_filter-avx.dir/build.make src/CMakeFiles/a3m_database_filter-avx.dir/build -make -f src/CMakeFiles/a3m_reduce-avx.dir/build.make src/CMakeFiles/a3m_reduce-avx.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f src/CMakeFiles/a3m_database_reduce-avx.dir/build.make src/CMakeFiles/a3m_database_reduce-avx.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 36%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 37%] Building CXX object src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o.d -o 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src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 38%] Building CXX object src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o [ 38%] Building CXX object src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -[ 38%] Built target ffindex_unpack -[ 38%] Built target ffindex_from_fasta +[ 39%] Building CXX object src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o +[ 39%] Building CXX object src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o +[ 40%] Building CXX object src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 38%] Built target ffindex_get -[ 38%] Built target ffindex_order -[ 38%] Built target ffindex_build -[ 39%] Building CXX object src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -[ 40%] Building CXX object src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -[ 40%] Built target ffindex_apply -[ 40%] Built target ffindex_modify -[ 40%] Built target ffindex_from_fasta_with_split -[ 40%] Built target ffindex_reduce -[ 41%] Linking CXX static library libhhviterbialgorithm_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -[ 42%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 -[ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp +[ 41%] Linking CXX static library libCS_OBJECTS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 +[ 42%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 43%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -[ 43%] Built target hhviterbialgorithm_and_ss +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h +[ 44%] Linking CXX static library libhhviterbialgorithm_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o +/usr/bin/ranlib libCS_OBJECTS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 43%] Built target hhviterbialgorithm_with_celloff_and_ss -/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 43%] Built target hhviterbialgorithm_with_celloff -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.lib.h -[ 44%] Linking CXX static library libCS_OBJECTS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h [ 45%] Linking CXX executable a3m_reduce-avx -[ 46%] Linking CXX executable a3m_extract-avx cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-avx.dir/link.txt --verbose=1 +[ 46%] Linking CXX executable a3m_extract-avx cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-avx.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated/context_data.crf.h.tmp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx.dir/link.d "CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-avx.dir/link.d "CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o" -o a3m_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 46%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 46%] Built target CS_OBJECTS +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a +[ 46%] Built target hhviterbialgorithm_with_celloff +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' [ 47%] Linking CXX executable a3m_database_reduce-avx cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-avx.dir/link.txt --verbose=1 -/usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o -/usr/bin/ranlib libCS_OBJECTS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' [ 48%] Linking CXX executable a3m_database_extract-avx cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-avx.dir/link.txt --verbose=1 -[ 48%] Built target CS_OBJECTS -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-avx.dir/link.d "CMakeFiles/a3m_extract-avx.dir/a3m_extract.cpp.o" -o a3m_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-avx.dir/link.d "CMakeFiles/a3m_reduce-avx.dir/a3m_reduce.cpp.o" -o a3m_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +[ 48%] Built target hhviterbialgorithm_and_ss +[ 48%] Built target a3m_reduce-avx +[ 48%] Built target a3m_extract-avx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-avx.dir/link.d "CMakeFiles/a3m_database_reduce-avx.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-avx.dir/link.d "CMakeFiles/a3m_database_extract-avx.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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&& /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp -[ 72%] Building CXX object 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp @@ -2193,11 +2234,6 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp -[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-avx.dir/link.d "CMakeFiles/a3m_database_filter-avx.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-avx ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 78%] Built target a3m_database_filter-avx /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -2237,24 +2273,24 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits-avx.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhalign-avx.dir/build.make src/CMakeFiles/hhalign-avx.dir/depend -make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhmake-avx.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/depend +make -f src/CMakeFiles/cstranslate-avx.dir/build.make src/CMakeFiles/cstranslate-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhfilter-avx.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/cstranslate-avx.dir/build.make src/CMakeFiles/cstranslate-avx.dir/depend +make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhsearch-avx.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_omp-avx.dir/build.make src/CMakeFiles/hhblits_omp-avx.dir/depend +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign-avx.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch_omp-avx.dir/build.make src/CMakeFiles/hhsearch_omp-avx.dir/depend -make -f src/CMakeFiles/hhalign_omp-avx.dir/build.make src/CMakeFiles/hhalign_omp-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f src/CMakeFiles/hhalign_omp-avx.dir/build.make src/CMakeFiles/hhalign_omp-avx.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhconsensus-avx.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhalign-avx.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/cstranslate-avx.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_ca3m-avx.dir/build.make src/CMakeFiles/hhblits_ca3m-avx.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src/CMakeFiles/hhblits_omp-avx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' @@ -2267,63 +2303,61 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f src/CMakeFiles/hhalign-avx.dir/build.make src/CMakeFiles/hhalign-avx.dir/build make -f src/CMakeFiles/hhblits-avx.dir/build.make src/CMakeFiles/hhblits-avx.dir/build make -f src/CMakeFiles/hhmake-avx.dir/build.make src/CMakeFiles/hhmake-avx.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhfilter-avx.dir/build.make src/CMakeFiles/hhfilter-avx.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' make -f src/CMakeFiles/hhsearch-avx.dir/build.make src/CMakeFiles/hhsearch-avx.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make -f src/CMakeFiles/hhconsensus-avx.dir/build.make src/CMakeFiles/hhconsensus-avx.dir/build make[4]: Entering 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-fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhconsensus.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -MF CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate-avx.dir/cs/cstranslate_app.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc -[ 91%] Linking CXX executable hhblits-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx.dir/link.txt --verbose=1 -/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': -/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] - 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); - | ^~~~~~~~ +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o -MF CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o.d -o CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_app.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-avx.dir/hhmake.cpp.o -MF CMakeFiles/hhmake-avx.dir/hhmake.cpp.o.d -o CMakeFiles/hhmake-avx.dir/hhmake.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmake.cpp +/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': +/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] + 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); + | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2335,11 +2369,10 @@ from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, - from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, - from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: + from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, - inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: + inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, + inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2347,8 +2380,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 92%] Linking CXX executable hhalign-avx +[ 93%] Linking CXX executable hhsearch-avx +[ 93%] Linking CXX executable hhalign-avx +[ 93%] Linking CXX executable hhblits-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-avx.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-avx.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -2376,15 +2413,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhsearch_omp-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-avx.dir/link.d "CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o" -o hhblits-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 93%] Built target hhblits-avx -[ 94%] Linking CXX executable hhsearch-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-avx.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable hhalign_omp-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -2412,31 +2440,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable hhfilter-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx.dir/link.d "CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o" -o hhalign-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 96%] Built target hhalign-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-avx.dir/link.d "CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 97%] Linking CXX executable hhblits_omp-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx.dir/link.txt --verbose=1 -[ 97%] Built target hhsearch_omp-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-avx.dir/link.d "CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o" -o hhfilter-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 97%] Built target hhfilter-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx.dir/link.d "CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 97%] Built target hhalign_omp-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-avx.dir/link.d "CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o" -o hhsearch-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 97%] Built target hhsearch-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx.dir/link.d "CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': -/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] - 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); - | ^~~~~~~~ +/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': +/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] + 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); + | ^~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/14/cstdio:42, from /usr/include/c++/14/ext/string_conversions.h:45, @@ -2448,10 +2455,11 @@ from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.h:11, - from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: + from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.h:34, + from /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, - inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: + inlined from 'void OutputFFIndex::close()' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, + inlined from 'int main(int, const char**)' at /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2459,19 +2467,47 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable hhconsensus-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx.dir/link.txt --verbose=1 -[ 98%] Built target hhblits_omp-avx -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx.dir/link.d "CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o" -o hhconsensus-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 95%] Linking CXX executable hhsearch_omp-avx +[ 95%] Linking CXX executable hhalign_omp-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-avx.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-avx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-avx.dir/link.d "CMakeFiles/hhsearch-avx.dir/hhblits_app.cpp.o" -o hhsearch-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' -[ 99%] Linking CXX executable hhmake-avx -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx.dir/link.txt --verbose=1 -[ 99%] Built target hhconsensus-avx -[100%] Linking CXX executable hhblits_ca3m-avx +[ 96%] Linking CXX executable hhblits_omp-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-avx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-avx.dir/link.d "CMakeFiles/hhblits-avx.dir/hhblits_app.cpp.o" -o hhblits-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-avx.dir/link.d "CMakeFiles/hhalign-avx.dir/hhblits_app.cpp.o" -o hhalign-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[ 97%] Linking CXX executable hhblits_ca3m-avx cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-avx.dir/link.txt --verbose=1 +[ 98%] Linking CXX executable hhmake-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-avx.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable hhfilter-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-avx.dir/link.txt --verbose=1 +[100%] Linking CXX executable hhconsensus-avx +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-avx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-avx.dir/link.d "CMakeFiles/hhfilter-avx.dir/hhfilter.cpp.o" -o hhfilter-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-avx.dir/link.d "CMakeFiles/hhsearch_omp-avx.dir/hhblits_omp.cpp.o" -o hhsearch_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-avx.dir/link.d "CMakeFiles/hhalign_omp-avx.dir/hhblits_omp.cpp.o" -o hhalign_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-avx.dir/link.d "CMakeFiles/hhblits_omp-avx.dir/hhblits_omp.cpp.o" -o hhblits_omp-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-avx.dir/link.d "CMakeFiles/hhmake-avx.dir/hhmake.cpp.o" -o hhmake-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-avx.dir/link.d "CMakeFiles/hhconsensus-avx.dir/hhconsensus.cpp.o" -o hhconsensus-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' +[100%] Built target hhalign_omp-avx +[100%] Built target hhblits-avx [100%] Built target hhmake-avx +[100%] Built target hhblits_omp-avx +[100%] Built target hhsearch_omp-avx +[100%] Built target hhfilter-avx +[100%] Built target hhalign-avx +[100%] Built target hhsearch-avx +[100%] Built target hhconsensus-avx /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-avx.dir/link.d "CMakeFiles/hhblits_ca3m-avx.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-avx libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' [100%] Built target hhblits_ca3m-avx @@ -2483,7 +2519,7 @@ make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_avx/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' - cd build_sse4.1 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_sse4.1 && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1//CMakeFiles/progress.marks @@ -2499,9 +2535,9 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/data /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' @@ -2515,57 +2551,57 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build +make -f 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src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing 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object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o +[ 10%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +[ 10%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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-include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc [ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h [ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc -[ 15%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/cs219.lib.h /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': @@ -2593,75 +2629,75 @@ make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 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argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); @@ -2669,88 +2705,79 @@ | | | | long long int int64_t {aka long int} | %ld -[ 26%] Linking C executable ffindex_unpack +[ 26%] Linking CXX static library libhhviterbialgorithm_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake +[ 27%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +[ 28%] Linking CXX static library libA3M_COMPRESS.a +cd 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-Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_reduce.dir/link.d CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -[ 33%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -[ 34%] Linking CXX static library libhhviterbialgorithm_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -[ 35%] Built target ffindex_order -[ 35%] Built target ffindex_build -[ 35%] Built target ffindex_get -[ 35%] Built target ffindex_reduce -[ 38%] Built target ffindex_unpack -[ 38%] Linking C executable ffindex_from_fasta_with_split -[ 38%] Linking CXX static library libA3M_COMPRESS.a -[ 38%] Linking C executable ffindex_apply -[ 36%] Built target ffindex_from_fasta -[ 38%] Linking C executable ffindex_modify -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration 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ffindex_from_fasta_with_split -[ 38%] Built target ffindex_apply -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp -/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a -/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -/usr/bin/ranlib libA3M_COMPRESS.a -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a -/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.lib.h -[ 38%] Built target hhviterbialgorithm_with_celloff_and_ss -[ 38%] Built target A3M_COMPRESS -[ 38%] Built target hhviterbialgorithm_with_celloff -[ 38%] Built target hhviterbialgorithm_and_ss +[ 39%] Built target A3M_COMPRESS make -f src/CMakeFiles/a3m_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_extract-sse4.1.dir/depend make -f src/CMakeFiles/a3m_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_reduce-sse4.1.dir/depend make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/depend make -f src/CMakeFiles/a3m_database_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_database_extract-sse4.1.dir/depend +make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_extract-sse4.1.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/a3m_reduce-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' @@ -2762,11 +2789,11 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build make -f src/CMakeFiles/a3m_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_extract-sse4.1.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_reduce-sse4.1.dir/build -make -f src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build.make src/CMakeFiles/a3m_database_reduce-sse4.1.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/a3m_database_extract-sse4.1.dir/build.make src/CMakeFiles/a3m_database_extract-sse4.1.dir/build make -f src/CMakeFiles/a3m_database_filter-sse4.1.dir/build.make src/CMakeFiles/a3m_database_filter-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' @@ -2774,50 +2801,59 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -[ 43%] Building CXX object src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -[ 43%] Building CXX object src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o +[ 40%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o +[ 41%] Building CXX object src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o +[ 42%] Building CXX object src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp [ 43%] Building CXX object src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -[ 43%] Building CXX object src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -[ 44%] Linking CXX static library libCS_OBJECTS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp +[ 44%] Building CXX object src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp +[ 44%] Built target ffindex_modify +[ 44%] Built target ffindex_reduce +[ 44%] Built target hhviterbialgorithm_and_ss +[ 44%] Built target ffindex_order +[ 44%] Built target ffindex_from_fasta_with_split +[ 44%] Built target hhviterbialgorithm_with_celloff +[ 44%] Built target ffindex_from_fasta +[ 44%] Built target ffindex_build +[ 44%] Built target ffindex_unpack +[ 44%] Built target ffindex_apply +[ 44%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 44%] Built target ffindex_get cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp -[ 45%] Linking CXX executable a3m_reduce-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse4.1.dir/link.txt --verbose=1 -[ 46%] Linking CXX executable a3m_extract-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse4.1.dir/link.txt --verbose=1 -[ 47%] Linking CXX executable a3m_database_reduce-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse4.1.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +[ 47%] Linking CXX executable a3m_database_reduce-sse4.1 +[ 47%] Linking CXX executable a3m_extract-sse4.1 +[ 47%] Linking CXX executable a3m_reduce-sse4.1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse4.1.dir/link.txt --verbose=1 [ 48%] Linking CXX executable a3m_database_extract-sse4.1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse4.1.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h +[ 48%] Built target CS_OBJECTS /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-sse4.1.dir/link.d "CMakeFiles/a3m_extract-sse4.1.dir/a3m_extract.cpp.o" -o a3m_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-sse4.1.dir/link.d "CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-sse4.1.dir/link.d "CMakeFiles/a3m_reduce-sse4.1.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-sse4.1.dir/link.d "CMakeFiles/a3m_database_reduce-sse4.1.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' [ 49%] Linking CXX executable a3m_database_filter-sse4.1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse4.1.dir/link.txt --verbose=1 -[ 49%] Built target a3m_database_reduce-sse4.1 -[ 49%] Built target a3m_extract-sse4.1 +[ 49%] Built target a3m_database_extract-sse4.1 [ 49%] Built target a3m_reduce-sse4.1 -[ 49%] Built target CS_OBJECTS -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-sse4.1.dir/link.d "CMakeFiles/a3m_database_extract-sse4.1.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +[ 49%] Built target a3m_extract-sse4.1 +[ 49%] Built target a3m_database_reduce-sse4.1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated/context_data.crf.h /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-sse4.1.dir/link.d "CMakeFiles/a3m_database_filter-sse4.1.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-sse4.1 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' [ 49%] Built target a3m_database_filter-sse4.1 -[ 49%] Built target a3m_database_extract-sse4.1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' [ 49%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend @@ -2826,64 +2862,64 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && 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CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o +[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o +[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -[ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp +[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp +[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o +[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -2919,30 +2955,30 @@ make -f src/CMakeFiles/hhblits-sse4.1.dir/build.make src/CMakeFiles/hhblits-sse4.1.dir/depend make -f src/CMakeFiles/hhmake-sse4.1.dir/build.make src/CMakeFiles/hhmake-sse4.1.dir/depend make -f src/CMakeFiles/hhfilter-sse4.1.dir/build.make src/CMakeFiles/hhfilter-sse4.1.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits-sse4.1.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make src/CMakeFiles/hhsearch-sse4.1.dir/depend make -f src/CMakeFiles/hhalign-sse4.1.dir/build.make src/CMakeFiles/hhalign-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhmake-sse4.1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits-sse4.1.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhconsensus-sse4.1.dir/build.make src/CMakeFiles/hhconsensus-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhfilter-sse4.1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhmake-sse4.1.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch-sse4.1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhfilter-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhblits_omp-sse4.1.dir/build.make src/CMakeFiles/hhblits_omp-sse4.1.dir/depend +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch-sse4.1.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhalign-sse4.1.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch_omp-sse4.1.dir/build.make src/CMakeFiles/hhsearch_omp-sse4.1.dir/depend +make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhconsensus-sse4.1.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/depend +make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/cstranslate-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhblits_omp-sse4.1.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_ca3m-sse4.1.dir/build.make src/CMakeFiles/hhblits_ca3m-sse4.1.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src/CMakeFiles/hhsearch_omp-sse4.1.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' @@ -2955,19 +2991,24 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make -f src/CMakeFiles/hhfilter-sse4.1.dir/build.make src/CMakeFiles/hhfilter-sse4.1.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make src/CMakeFiles/hhsearch-sse4.1.dir/build make -f src/CMakeFiles/hhblits-sse4.1.dir/build.make src/CMakeFiles/hhblits-sse4.1.dir/build make -f src/CMakeFiles/hhmake-sse4.1.dir/build.make src/CMakeFiles/hhmake-sse4.1.dir/build +make -f src/CMakeFiles/hhfilter-sse4.1.dir/build.make src/CMakeFiles/hhfilter-sse4.1.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make -f src/CMakeFiles/hhsearch-sse4.1.dir/build.make src/CMakeFiles/hhsearch-sse4.1.dir/build make -f src/CMakeFiles/hhalign-sse4.1.dir/build.make src/CMakeFiles/hhalign-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhconsensus-sse4.1.dir/build.make src/CMakeFiles/hhconsensus-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhblits_omp-sse4.1.dir/build.make src/CMakeFiles/hhblits_omp-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make -f src/CMakeFiles/hhsearch_omp-sse4.1.dir/build.make src/CMakeFiles/hhsearch_omp-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make -f src/CMakeFiles/hhalign_omp-sse4.1.dir/build.make src/CMakeFiles/hhalign_omp-sse4.1.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' @@ -2976,34 +3017,30 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make -f src/CMakeFiles/cstranslate-sse4.1.dir/build.make src/CMakeFiles/cstranslate-sse4.1.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -make -f src/CMakeFiles/hhsearch_omp-sse4.1.dir/build.make src/CMakeFiles/hhsearch_omp-sse4.1.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Entering directory 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CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +[ 91%] Linking CXX executable hhblits-sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3030,8 +3067,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 91%] Linking CXX executable hhsearch-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse4.1.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3059,14 +3095,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhblits-sse4.1 -[ 93%] Linking CXX executable hhalign-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse4.1.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse4.1.dir/link.txt --verbose=1 -[ 94%] Linking CXX executable hhalign_omp-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse4.1.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable hhblits_ca3m-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse4.1.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3094,36 +3122,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-sse4.1.dir/link.d "CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o" -o hhblits-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 95%] Built target hhblits-sse4.1 -[ 96%] Linking CXX executable hhsearch_omp-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse4.1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse4.1.dir/link.d "CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 98%] Linking CXX executable hhfilter-sse4.1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-sse4.1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-sse4.1.dir/link.d "CMakeFiles/hhalign-sse4.1.dir/hhblits_app.cpp.o" -o hhalign-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -[ 98%] Built target hhblits_ca3m-sse4.1 -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 98%] Built target hhalign-sse4.1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-sse4.1.dir/link.d "CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-sse4.1.dir/link.d "CMakeFiles/hhfilter-sse4.1.dir/hhfilter.cpp.o" -o hhfilter-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 98%] Built target hhsearch_omp-sse4.1 -[ 98%] Built target hhfilter-sse4.1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-sse4.1.dir/link.d "CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o" -o hhconsensus-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[ 98%] Built target hhconsensus-sse4.1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3151,16 +3149,54 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 99%] Linking CXX executable hhblits_omp-sse4.1 +[ 92%] Linking CXX executable hhalign-sse4.1 +[ 93%] Linking CXX executable hhsearch-sse4.1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse4.1.dir/link.txt --verbose=1 +[ 94%] Linking CXX executable hhblits_omp-sse4.1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse4.1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-sse4.1.dir/link.d "CMakeFiles/hhblits-sse4.1.dir/hhblits_app.cpp.o" -o hhblits-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +[ 94%] Built target hhblits-sse4.1 +[ 98%] Linking CXX executable hhfilter-sse4.1 +[ 98%] Linking CXX executable hhblits_ca3m-sse4.1 +[ 98%] Linking CXX executable hhsearch_omp-sse4.1 +[ 98%] Linking CXX executable hhalign_omp-sse4.1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-sse4.1.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse4.1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse4.1.dir/link.d "CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd 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../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-sse4.1.dir/link.d "CMakeFiles/hhfilter-sse4.1.dir/hhfilter.cpp.o" -o hhfilter-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +[ 98%] Built target hhalign-sse4.1 +[ 98%] Built target hhfilter-sse4.1 +[ 98%] Built target hhblits_omp-sse4.1 +[ 98%] Built target hhsearch-sse4.1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-sse4.1.dir/link.d "CMakeFiles/hhsearch_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' [100%] Linking CXX executable hhmake-sse4.1 +[100%] Linking CXX executable hhconsensus-sse4.1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse4.1.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse4.1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse4.1.dir/link.d "CMakeFiles/hhblits_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse4.1.dir/link.d "CMakeFiles/hhblits_ca3m-sse4.1.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-sse4.1.dir/link.d "CMakeFiles/hhalign_omp-sse4.1.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' -[100%] Built target hhblits_omp-sse4.1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-sse4.1.dir/link.d "CMakeFiles/hhconsensus-sse4.1.dir/hhconsensus.cpp.o" -o hhconsensus-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-sse4.1.dir/link.d "CMakeFiles/hhmake-sse4.1.dir/hhmake.cpp.o" -o hhmake-sse4.1 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' +[100%] Built target hhsearch_omp-sse4.1 [100%] Built target hhmake-sse4.1 +[100%] Built target hhblits_ca3m-sse4.1 +[100%] Built target hhalign_omp-sse4.1 +[100%] Built target hhconsensus-sse4.1 [100%] Linking CXX executable cstranslate-sse4.1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-sse4.1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-sse4.1.dir/link.d "CMakeFiles/cstranslate-sse4.1.dir/cs/cstranslate_app.cc.o" -o cstranslate-sse4.1 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -3169,7 +3205,7 @@ make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' - cd build_ssse3 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_ssse3 && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3//CMakeFiles/progress.marks @@ -3179,9 +3215,9 @@ make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend +make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/data /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend @@ -3199,59 +3235,59 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 4%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -[ 4%] Generating ../generated/cs219.lib.h -[ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -[ 6%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -[ 7%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -[ 11%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -[ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -[ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -[ 15%] Generating ../generated/context_data.crf.h -[ 15%] 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src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc +[ 4%] Generating ../generated/context_data.crf.h +[ 5%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +[ 7%] Generating ../generated/cs219.lib.h +[ 7%] Generating ../generated/context_data.lib.h +[ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +[ 9%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc +[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/cs219.lib.h /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': @@ -3285,17 +3321,17 @@ make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake "--color=" @@ -3304,50 +3340,62 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' 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> /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.lib.h.tmp +/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +/usr/bin/ranlib libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp +[ 34%] Linking C executable ffindex_get +[ 34%] Linking C executable ffindex_modify +[ 34%] Linking C executable ffindex_build +[ 34%] Linking C executable ffindex_unpack +[ 35%] Linking C executable ffindex_reduce +[ 35%] Linking C executable ffindex_from_fasta +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt 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src/CMakeFiles/a3m_database_filter-ssse3.dir/depend cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_reduce-ssse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_reduce-ssse3.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/a3m_database_extract-ssse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' @@ -3450,59 +3471,74 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/build make -f src/CMakeFiles/a3m_extract-ssse3.dir/build.make src/CMakeFiles/a3m_extract-ssse3.dir/build make -f src/CMakeFiles/a3m_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_reduce-ssse3.dir/build -make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/a3m_database_reduce-ssse3.dir/build.make src/CMakeFiles/a3m_database_reduce-ssse3.dir/build make -f src/CMakeFiles/a3m_database_extract-ssse3.dir/build.make src/CMakeFiles/a3m_database_extract-ssse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/a3m_database_filter-ssse3.dir/build.make src/CMakeFiles/a3m_database_filter-ssse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -[ 39%] Building CXX object src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -[ 42%] Building CXX object src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -[ 42%] Building CXX object src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -[ 42%] Building CXX object src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -[ 43%] Building CXX object src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h +[ 44%] Building CXX object src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o +[ 40%] Building CXX object src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o +[ 44%] Building CXX object src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o +[ 44%] Building CXX object src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o +[ 44%] Linking CXX static library libCS_OBJECTS.a +[ 44%] Building CXX object src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -[ 44%] Linking CXX static library libCS_OBJECTS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 44%] Built target ffindex_get +[ 44%] Built target ffindex_order +[ 44%] Built target ffindex_build +[ 44%] Built target hhviterbialgorithm_and_ss +[ 44%] Built target ffindex_unpack +[ 44%] Built target ffindex_reduce +[ 44%] Built target ffindex_apply +[ 44%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 44%] Built target hhviterbialgorithm_with_celloff +[ 44%] Built target ffindex_from_fasta_with_split +[ 44%] Built target ffindex_from_fasta +[ 44%] Built target ffindex_modify cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated/context_data.crf.h [ 44%] Built target CS_OBJECTS -[ 48%] Linking CXX executable a3m_extract-ssse3 -[ 48%] Linking CXX executable a3m_reduce-ssse3 -[ 48%] Linking CXX executable a3m_database_reduce-ssse3 -[ 48%] Linking CXX executable a3m_database_extract-ssse3 +[ 46%] Linking CXX executable a3m_extract-ssse3 +[ 46%] Linking CXX executable a3m_reduce-ssse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-ssse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-ssse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-ssse3.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-ssse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-ssse3.dir/link.d "CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-ssse3.dir/link.d "CMakeFiles/a3m_reduce-ssse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-ssse3.dir/link.d "CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o" -o a3m_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-ssse3.dir/link.d "CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-ssse3.dir/link.d "CMakeFiles/a3m_extract-ssse3.dir/a3m_extract.cpp.o" -o a3m_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 46%] Built target a3m_extract-ssse3 +[ 46%] Built target a3m_reduce-ssse3 +[ 49%] Linking CXX executable a3m_database_reduce-ssse3 [ 49%] Linking CXX executable a3m_database_filter-ssse3 +[ 49%] Linking CXX executable a3m_database_extract-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-ssse3.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-ssse3.dir/link.txt --verbose=1 -[ 49%] Built target a3m_database_reduce-ssse3 -[ 49%] Built target a3m_extract-ssse3 -[ 49%] Built target a3m_reduce-ssse3 -[ 49%] Built target a3m_database_extract-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-ssse3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-ssse3.dir/link.d "CMakeFiles/a3m_database_reduce-ssse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-ssse3.dir/link.d "CMakeFiles/a3m_database_extract-ssse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-ssse3.dir/link.d "CMakeFiles/a3m_database_filter-ssse3.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-ssse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 49%] Built target a3m_database_extract-ssse3 +[ 49%] Built target a3m_database_reduce-ssse3 [ 49%] Built target a3m_database_filter-ssse3 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' [ 49%] Built target generated @@ -3513,63 +3549,63 @@ make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o +[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o +[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp +[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o +[ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp -[ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o +[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o +[ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp +[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o +[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o +[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o +[ 70%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o +[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o +[ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +[ 78%] Building CXX object 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp -[ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp -[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp -[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -[ 75%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && 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-I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdatabase.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhalfalignment.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -3606,27 +3642,27 @@ make -f src/CMakeFiles/hhmake-ssse3.dir/build.make src/CMakeFiles/hhmake-ssse3.dir/depend make -f src/CMakeFiles/hhfilter-ssse3.dir/build.make src/CMakeFiles/hhfilter-ssse3.dir/depend make -f src/CMakeFiles/hhsearch-ssse3.dir/build.make src/CMakeFiles/hhsearch-ssse3.dir/depend +make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits-ssse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhmake-ssse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/depend +make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhfilter-ssse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/depend make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/depend +make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhsearch-ssse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhalign-ssse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch_omp-ssse3.dir/build.make src/CMakeFiles/hhsearch_omp-ssse3.dir/depend +make -f src/CMakeFiles/hhalign_omp-ssse3.dir/build.make src/CMakeFiles/hhalign_omp-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhconsensus-ssse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhalign_omp-ssse3.dir/build.make src/CMakeFiles/hhalign_omp-ssse3.dir/depend +make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/cstranslate-ssse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_omp-ssse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' @@ -3637,59 +3673,61 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src/CMakeFiles/hhblits_ca3m-ssse3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/hhfilter-ssse3.dir/build.make src/CMakeFiles/hhfilter-ssse3.dir/build -make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/hhsearch-ssse3.dir/build.make src/CMakeFiles/hhsearch-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhblits-ssse3.dir/build.make src/CMakeFiles/hhblits-ssse3.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhmake-ssse3.dir/build.make src/CMakeFiles/hhmake-ssse3.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/build +make -f src/CMakeFiles/hhfilter-ssse3.dir/build.make src/CMakeFiles/hhfilter-ssse3.dir/build +make -f src/CMakeFiles/hhalign-ssse3.dir/build.make src/CMakeFiles/hhalign-ssse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/hhconsensus-ssse3.dir/build.make src/CMakeFiles/hhconsensus-ssse3.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/cstranslate-ssse3.dir/build.make src/CMakeFiles/cstranslate-ssse3.dir/build +make -f src/CMakeFiles/hhblits_omp-ssse3.dir/build.make src/CMakeFiles/hhblits_omp-ssse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make -f src/CMakeFiles/hhsearch_omp-ssse3.dir/build.make src/CMakeFiles/hhsearch_omp-ssse3.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/hhsearch-ssse3.dir/build.make src/CMakeFiles/hhsearch-ssse3.dir/build make -f src/CMakeFiles/hhalign_omp-ssse3.dir/build.make src/CMakeFiles/hhalign_omp-ssse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make -f src/CMakeFiles/hhblits_ca3m-ssse3.dir/build.make src/CMakeFiles/hhblits_ca3m-ssse3.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -[ 81%] Building CXX object src/CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o -[ 81%] Building CXX object src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o +[ 80%] Building CXX object src/CMakeFiles/hhmake-ssse3.dir/hhmake.cpp.o +[ 81%] Building CXX object src/CMakeFiles/hhblits-ssse3.dir/hhblits_app.cpp.o [ 82%] Building CXX object src/CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o -MF CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o.d -o CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o -c 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-D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhconsensus.cpp +[ 91%] Linking CXX executable hhalign-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-ssse3.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3717,9 +3755,9 @@ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable hhblits-ssse3 -[ 92%] Linking CXX executable hhalign-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-ssse3.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-ssse3.dir/link.txt --verbose=1 +[ 93%] Linking CXX executable hhsearch-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-ssse3.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3747,21 +3785,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhsearch-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-ssse3.dir/link.txt --verbose=1 -[ 94%] Linking CXX executable hhblits_ca3m-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-ssse3.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable hhblits_omp-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-ssse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-ssse3.dir/link.d "CMakeFiles/hhblits-ssse3.dir/hhblits_app.cpp.o" -o hhblits-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-ssse3.dir/link.d "CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o" -o hhalign-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-ssse3.dir/link.d "CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o" -o hhsearch-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -[ 95%] Built target hhsearch-ssse3 -[ 95%] Built target hhblits-ssse3 -[ 95%] Built target hhalign-ssse3 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3789,8 +3812,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable hhmake-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-ssse3.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -3818,35 +3839,50 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-ssse3.dir/link.d "CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 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-fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-ssse3.dir/link.d "CMakeFiles/hhalign-ssse3.dir/hhblits_app.cpp.o" -o hhalign-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 94%] Linking CXX executable hhblits_ca3m-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-ssse3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-ssse3.dir/link.d "CMakeFiles/hhblits-ssse3.dir/hhblits_app.cpp.o" -o hhblits-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' -[ 96%] Built target hhblits_omp-ssse3 -[ 96%] Built target hhblits_ca3m-ssse3 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-ssse3.dir/link.d "CMakeFiles/hhmake-ssse3.dir/hhmake.cpp.o" -o hhmake-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 96%] Linking CXX executable hhalign_omp-ssse3 +[ 96%] Linking CXX executable hhsearch_omp-ssse3 +[ 96%] Built target hhblits-ssse3 +[ 96%] Built target hhalign-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-ssse3.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-ssse3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-ssse3.dir/link.d "CMakeFiles/hhsearch-ssse3.dir/hhblits_app.cpp.o" -o hhsearch-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[ 96%] Built target hhsearch-ssse3 +[ 97%] Linking CXX executable hhblits_omp-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-ssse3.dir/link.txt --verbose=1 +[ 98%] Linking CXX executable hhmake-ssse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-ssse3.dir/link.txt --verbose=1 [ 99%] Linking CXX executable hhconsensus-ssse3 -[ 99%] Linking CXX executable hhalign_omp-ssse3 -[ 99%] Linking CXX executable hhsearch_omp-ssse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-ssse3.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-ssse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-ssse3.dir/link.txt --verbose=1 [100%] Linking CXX executable hhfilter-ssse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-ssse3.dir/link.txt --verbose=1 -[100%] Built target hhmake-ssse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-ssse3.dir/link.d "CMakeFiles/hhfilter-ssse3.dir/hhfilter.cpp.o" -o hhfilter-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target hhfilter-ssse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-ssse3.dir/link.d "CMakeFiles/hhsearch_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-ssse3.dir/link.d "CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-ssse3.dir/link.d "CMakeFiles/hhconsensus-ssse3.dir/hhconsensus.cpp.o" -o hhconsensus-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' [100%] Built target hhsearch_omp-ssse3 -[100%] Built target hhalign_omp-ssse3 [100%] Built target hhconsensus-ssse3 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-ssse3.dir/link.d "CMakeFiles/hhalign_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-ssse3.dir/link.d "CMakeFiles/hhmake-ssse3.dir/hhmake.cpp.o" -o hhmake-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-ssse3.dir/link.d "CMakeFiles/hhblits_ca3m-ssse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[100%] Built target hhalign_omp-ssse3 +[100%] Built target hhmake-ssse3 +[100%] Built target hhblits_ca3m-ssse3 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-ssse3.dir/link.d "CMakeFiles/hhblits_omp-ssse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-ssse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' +[100%] Built target hhblits_omp-ssse3 [100%] Linking CXX executable cstranslate-ssse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-ssse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-ssse3.dir/link.d "CMakeFiles/cstranslate-ssse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-ssse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -3855,7 +3891,7 @@ make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' - cd build_sse3 && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_sse3 && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3//CMakeFiles/progress.marks @@ -3871,9 +3907,9 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/data /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' @@ -3884,60 +3920,60 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -[ 9%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -[ 11%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -[ 12%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -[ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -[ 15%] Generating ../generated/cs219.lib.h -[ 15%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -[ 15%] Generating ../generated/context_data.crf.h -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -[ 15%] Generating ../generated/context_data.lib.h -[ 1%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +[ 3%] Generating ../generated/context_data.lib.h +[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +[ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 4%] Generating ../generated/context_data.crf.h +[ 5%] Generating ../generated/cs219.lib.h +[ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +[ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 9%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc +[ 10%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o 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CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c +[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection 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-fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc +[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o +[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/cs219.lib.h /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': @@ -3958,10 +3994,31 @@ [ 16%] Linking C static library libffindex.a cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 +[ 18%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a +[ 19%] Linking CXX static library libhhviterbialgorithm_and_ss.a +[ 19%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 16%] Built target ffindex +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 19%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 19%] Built target ffindex +[ 19%] Built target hhviterbialgorithm_with_celloff +[ 19%] Built target hhviterbialgorithm_and_ss make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend @@ -3975,9 +4032,9 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend +make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend @@ -3989,51 +4046,54 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake "--color=" +[ 20%] Linking CXX static library libA3M_COMPRESS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -[ 18%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o +[ 22%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o +[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o +[ 24%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o +[ 29%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c 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-O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta.c +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); @@ -4041,221 +4101,197 @@ | | | | long long int int64_t {aka long int} | %ld -[ 26%] Linking C executable ffindex_modify -[ 28%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -[ 28%] Linking C executable ffindex_order -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp +[ 36%] Linking C executable ffindex_get +[ 31%] Linking C executable ffindex_from_fasta_with_split +[ 32%] Linking C executable ffindex_order +[ 36%] Linking C executable ffindex_unpack +[ 34%] Linking C executable ffindex_reduce +[ 36%] Linking C executable ffindex_build +[ 36%] Linking C executable ffindex_modify cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -[ 29%] Linking C executable ffindex_unpack -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong 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ffindex_get libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 30%] Built target ffindex_order -[ 30%] Built target ffindex_unpack -[ 30%] Built target ffindex_modify -[ 30%] Built target ffindex_get -[ 36%] Linking C executable ffindex_reduce -[ 36%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -[ 36%] Linking C executable ffindex_from_fasta_with_split -[ 36%] Linking C executable ffindex_build -[ 36%] Linking C executable ffindex_apply -[ 36%] Linking CXX static library libA3M_COMPRESS.a -[ 37%] Linking C executable ffindex_from_fasta -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/lib/ffindex/src && 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'/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 40%] Building CXX object src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -[ 42%] Building CXX object src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o +[ 41%] Building CXX object src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o [ 42%] Building CXX object src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -[ 43%] Building CXX object src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp -[ 44%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp +[ 42%] Building CXX object src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 42%] Built target ffindex_modify +[ 42%] Built target ffindex_get +[ 42%] Built target ffindex_order +[ 42%] Built target ffindex_build +[ 42%] Built target ffindex_apply +[ 42%] Built target ffindex_from_fasta +[ 42%] Built target ffindex_from_fasta_with_split cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp +[ 42%] Built target ffindex_reduce +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp +make -f src/CMakeFiles/a3m_reduce-sse3.dir/build.make src/CMakeFiles/a3m_reduce-sse3.dir/build cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -[ 44%] Built target hhviterbialgorithm_with_celloff_and_ss -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.lib.h -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/a3m_extract-sse3.dir/build.make src/CMakeFiles/a3m_extract-sse3.dir/build +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 42%] Built target ffindex_unpack +[ 43%] Building CXX object src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o +[ 44%] Building CXX object src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp [ 44%] Built target CS_OBJECTS -[ 44%] Built target hhviterbialgorithm_and_ss -[ 46%] Linking CXX executable a3m_reduce-sse3 -[ 46%] Linking CXX executable a3m_extract-sse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse3.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h +[ 46%] Linking CXX executable a3m_database_extract-sse3 +[ 48%] Linking CXX executable a3m_reduce-sse3 +[ 47%] Linking CXX executable a3m_extract-sse3 +[ 48%] Linking CXX executable a3m_database_reduce-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse3.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-sse3.dir/link.txt --verbose=1 -[ 47%] Linking CXX executable a3m_database_reduce-sse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce-sse3.dir/link.txt --verbose=1 -[ 48%] Linking CXX executable a3m_database_extract-sse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-sse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-sse3.dir/link.d "CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o" -o a3m_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-sse3.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 49%] Linking CXX executable a3m_database_filter-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-sse3.dir/link.d "CMakeFiles/a3m_reduce-sse3.dir/a3m_reduce.cpp.o" -o a3m_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_reduce-sse3.dir/link.d "CMakeFiles/a3m_database_reduce-sse3.dir/a3m_database_reduce.cpp.o" -o a3m_database_reduce-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated/context_data.crf.h -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-sse3.dir/link.d "CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 48%] Built target a3m_database_extract-sse3 -[ 48%] Built target a3m_database_reduce-sse3 -[ 48%] Built target a3m_extract-sse3 -[ 48%] Built target a3m_reduce-sse3 -[ 49%] Linking CXX executable a3m_database_filter-sse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter-sse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_filter-sse3.dir/link.d "CMakeFiles/a3m_database_filter-sse3.dir/a3m_database_filter.cpp.o" -o a3m_database_filter-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_database_extract-sse3.dir/link.d "CMakeFiles/a3m_database_extract-sse3.dir/a3m_database_extract.cpp.o" -o a3m_database_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 49%] Built target a3m_database_filter-sse3 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_extract-sse3.dir/link.d "CMakeFiles/a3m_extract-sse3.dir/a3m_extract.cpp.o" -o a3m_extract-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 49%] Built target a3m_database_extract-sse3 +[ 49%] Built target a3m_database_reduce-sse3 +[ 49%] Built target a3m_reduce-sse3 [ 49%] Built target generated make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src 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-ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits.cpp -[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -[ 58%] Building CXX object 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a3m_database_filter-sse3 ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o +[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o +[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 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-I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp +[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhdecl.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalign.cpp +[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhhitlist.cpp -[ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp +[ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp cd 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp -[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd 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object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbirunner.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfunc.cpp +[ 78%] Built target a3m_database_filter-sse3 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhalignment.cpp:1797:39: warning: '%s' directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", @@ -4292,30 +4328,30 @@ make -f src/CMakeFiles/hhmake-sse3.dir/build.make src/CMakeFiles/hhmake-sse3.dir/depend make -f src/CMakeFiles/hhfilter-sse3.dir/build.make src/CMakeFiles/hhfilter-sse3.dir/depend make -f src/CMakeFiles/hhsearch-sse3.dir/build.make src/CMakeFiles/hhsearch-sse3.dir/depend +make -f src/CMakeFiles/hhalign-sse3.dir/build.make src/CMakeFiles/hhalign-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits-sse3.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhalign-sse3.dir/build.make src/CMakeFiles/hhalign-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhmake-sse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhconsensus-sse3.dir/build.make src/CMakeFiles/hhconsensus-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhfilter-sse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/cstranslate-sse3.dir/build.make src/CMakeFiles/cstranslate-sse3.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch-sse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhblits_omp-sse3.dir/build.make src/CMakeFiles/hhblits_omp-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign-sse3.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch-sse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/depend -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhconsensus-sse3.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhalign_omp-sse3.dir/build.make src/CMakeFiles/hhalign_omp-sse3.dir/depend -make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/cstranslate-sse3.dir/DependInfo.cmake "--color=" +make -f src/CMakeFiles/hhblits_ca3m-sse3.dir/build.make src/CMakeFiles/hhblits_ca3m-sse3.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhblits_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign-sse3.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhconsensus-sse3.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhsearch_omp-sse3.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src/CMakeFiles/hhalign_omp-sse3.dir/DependInfo.cmake "--color=" @@ -4324,58 +4360,58 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/hhmake-sse3.dir/build.make src/CMakeFiles/hhmake-sse3.dir/build make -f src/CMakeFiles/hhblits-sse3.dir/build.make src/CMakeFiles/hhblits-sse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/hhfilter-sse3.dir/build.make src/CMakeFiles/hhfilter-sse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/hhmake-sse3.dir/build.make src/CMakeFiles/hhmake-sse3.dir/build -make -f src/CMakeFiles/hhsearch-sse3.dir/build.make src/CMakeFiles/hhsearch-sse3.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/cstranslate-sse3.dir/build.make src/CMakeFiles/cstranslate-sse3.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhalign-sse3.dir/build.make src/CMakeFiles/hhalign-sse3.dir/build -make -f src/CMakeFiles/hhfilter-sse3.dir/build.make src/CMakeFiles/hhfilter-sse3.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/hhconsensus-sse3.dir/build.make src/CMakeFiles/hhconsensus-sse3.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/hhsearch-sse3.dir/build.make src/CMakeFiles/hhsearch-sse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/cstranslate-sse3.dir/build.make src/CMakeFiles/cstranslate-sse3.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -make -f src/CMakeFiles/hhblits_omp-sse3.dir/build.make src/CMakeFiles/hhblits_omp-sse3.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make -f src/CMakeFiles/hhconsensus-sse3.dir/build.make src/CMakeFiles/hhconsensus-sse3.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhsearch_omp-sse3.dir/build.make src/CMakeFiles/hhsearch_omp-sse3.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' make -f src/CMakeFiles/hhalign_omp-sse3.dir/build.make 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp +[ 90%] Building CXX object src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -4404,6 +4440,10 @@ | ~~~~~~~~~~~~~~~~~ [ 91%] Linking CXX executable hhalign-sse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-sse3.dir/link.txt --verbose=1 +[ 92%] Linking CXX executable hhsearch-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse3.dir/link.txt --verbose=1 +[ 93%] Linking CXX executable hhblits-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse3.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -4458,6 +4498,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +[ 94%] Linking CXX executable hhblits_ca3m-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse3.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -4485,54 +4527,48 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable hhblits-sse3 -[ 93%] Linking CXX executable hhsearch-sse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-sse3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-sse3.dir/link.d "CMakeFiles/hhblits-sse3.dir/hhblits_app.cpp.o" -o hhblits-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign-sse3.dir/link.d "CMakeFiles/hhalign-sse3.dir/hhblits_app.cpp.o" -o hhalign-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 93%] Built target hhalign-sse3 -[ 99%] Linking CXX executable hhalign_omp-sse3 -[ 99%] Linking CXX executable hhconsensus-sse3 -[ 99%] Linking CXX executable hhblits_ca3m-sse3 -[ 99%] Linking CXX executable hhsearch_omp-sse3 -[ 99%] Linking CXX executable hhmake-sse3 -[ 99%] Linking CXX executable hhblits_omp-sse3 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse3.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-sse3.dir/link.d "CMakeFiles/hhblits-sse3.dir/hhblits_app.cpp.o" -o hhblits-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch-sse3.dir/link.d "CMakeFiles/hhsearch-sse3.dir/hhblits_app.cpp.o" -o hhsearch-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 94%] Built target hhblits-sse3 make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 95%] Linking CXX executable hhsearch_omp-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-sse3.dir/link.txt --verbose=1 +[ 95%] Built target hhalign-sse3 +[ 95%] Built target hhsearch-sse3 +[ 96%] Linking CXX executable hhblits_omp-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp-sse3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse3.dir/link.d "CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[ 99%] Built target hhsearch-sse3 -[ 99%] Built target hhblits-sse3 -[100%] Linking CXX executable hhfilter-sse3 +[ 97%] Linking CXX executable hhfilter-sse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-sse3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-sse3.dir/link.d "CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o" -o hhmake-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse3.dir/link.d "CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-sse3.dir/link.d "CMakeFiles/hhblits_ca3m-sse3.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +[ 98%] Linking CXX executable hhalign_omp-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-sse3.dir/link.d "CMakeFiles/hhsearch_omp-sse3.dir/hhblits_omp.cpp.o" -o hhsearch_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 98%] Built target hhsearch_omp-sse3 +[ 98%] Built target hhblits_ca3m-sse3 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-sse3.dir/link.d "CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o" -o hhfilter-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[ 98%] Built target hhfilter-sse3 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-sse3.dir/link.d "CMakeFiles/hhblits_omp-sse3.dir/hhblits_omp.cpp.o" -o hhblits_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[100%] Linking CXX executable hhmake-sse3 +[100%] Linking CXX executable hhconsensus-sse3 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-sse3.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-sse3.dir/link.txt --verbose=1 +[100%] Built target hhblits_omp-sse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-sse3.dir/link.d "CMakeFiles/hhalign_omp-sse3.dir/hhblits_omp.cpp.o" -o hhalign_omp-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' +[100%] Built target hhalign_omp-sse3 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-sse3.dir/link.d "CMakeFiles/hhconsensus-sse3.dir/hhconsensus.cpp.o" -o hhconsensus-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-sse3.dir/link.d "CMakeFiles/hhfilter-sse3.dir/hhfilter.cpp.o" -o hhfilter-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-sse3.dir/link.d "CMakeFiles/hhmake-sse3.dir/hhmake.cpp.o" -o hhmake-sse3 libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' -[100%] Built target hhblits_omp-sse3 -[100%] Built target hhsearch_omp-sse3 -[100%] Built target hhblits_ca3m-sse3 -[100%] Built target hhalign_omp-sse3 -[100%] Built target hhmake-sse3 [100%] Built target hhconsensus-sse3 -[100%] Built target hhfilter-sse3 +[100%] Built target hhmake-sse3 [100%] Linking CXX executable cstranslate-sse3 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-sse3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-sse3.dir/link.d "CMakeFiles/cstranslate-sse3.dir/cs/cstranslate_app.cc.o" -o cstranslate-sse3 libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -4541,7 +4577,7 @@ make[3]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_sse3/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' - cd build_plain && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build_plain && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/build_plain//CMakeFiles/progress.marks @@ -4554,15 +4590,15 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend -make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/data /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/data /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/data/CMakeFiles/generated.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake "--color=" @@ -4571,59 +4607,59 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' 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directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -[ 2%] Generating ../generated/context_data.crf.h -[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +[ 3%] Generating ../generated/context_data.lib.h +[ 5%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +[ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +[ 7%] Generating ../generated/cs219.lib.h +[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o +[ 6%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o +[ 6%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +[ 15%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +[ 6%] Generating ../generated/context_data.crf.h +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o +[ 15%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF CMakeFiles/ffindex.dir/ffindex.c.o.d -o CMakeFiles/ffindex.dir/ffindex.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c -[ 7%] Generating ../generated/cs219.lib.h -[ 7%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -[ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -[ 8%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -[ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/aa.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF CMakeFiles/ffindex.dir/ffutil.c.o.d -o CMakeFiles/ffindex.dir/ffutil.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c -[ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc -[ 11%] Generating ../generated/context_data.lib.h -[ 11%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -[ 12%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/as.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/log.cc -[ 15%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/cs/application.cc +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/cs219.lib.h /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_compress.cpp: In function 'std::string& rtrim(std::string&)': @@ -4654,18 +4690,18 @@ make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake "--color=" +make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake "--color=" -make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend -make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds 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lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build 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&& /usr/bin/cc -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cc 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/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c +[ 27%] Linking CXX static library libhhviterbialgorithm_and_ss.a +[ 27%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +[ 28%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry': /build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_apply_mpi.c:172:53: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'int64_t' {aka 'long int'} [-Wformat=] 172 | fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); @@ -4727,82 +4771,82 @@ | | | | long long int int64_t {aka long int} | %ld -[ 26%] Linking C executable ffindex_unpack -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 -[ 27%] Linking C executable ffindex_get -[ 28%] Linking C executable ffindex_order -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -[ 29%] Linking C executable ffindex_reduce -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 -[ 30%] Linking C executable ffindex_modify +/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[ 31%] Linking C executable ffindex_reduce +[ 30%] Linking C executable ffindex_get +[ 31%] Built target hhviterbialgorithm_and_ss +[ 31%] Linking C executable ffindex_modify +[ 31%] Built target hhviterbialgorithm_with_celloff cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -[ 31%] Linking C executable ffindex_from_fasta +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 +[ 32%] Linking C executable ffindex_from_fasta cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 32%] Linking C executable ffindex_build +[ 33%] Linking C executable ffindex_unpack +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 +[ 36%] Linking C executable ffindex_from_fasta_with_split +[ 35%] Linking C executable ffindex_order +[ 36%] Linking C executable ffindex_build +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 +/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp +[ 36%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 37%] Linking C executable ffindex_apply +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_unpack.dir/link.d CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a /usr/bin/cc 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_get.dir/link.d CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a -[ 32%] Built target ffindex_unpack make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_modify.dir/link.d CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 33%] Linking C executable ffindex_from_fasta_with_split -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 -[ 33%] Built target ffindex_order -[ 33%] Built target ffindex_from_fasta -[ 33%] Built target ffindex_get -[ 33%] Built target ffindex_reduce -[ 33%] Built target ffindex_modify -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 34%] Linking C executable ffindex_apply -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 -[ 34%] Built target ffindex_build +[ 38%] Linking CXX static library libA3M_COMPRESS.a +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake +[ 38%] Built target ffindex_unpack +[ 38%] Built target ffindex_from_fasta +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 +[ 38%] Built target ffindex_get +[ 38%] Built target ffindex_reduce +[ 38%] Built target ffindex_modify +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_order.dir/link.d CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a /usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_from_fasta_with_split.dir/link.d CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 34%] Built target ffindex_from_fasta_with_split -/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 34%] Built target ffindex_apply -[ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 -[ 36%] Linking CXX static library libA3M_COMPRESS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake -[ 37%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 -/usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff.a +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_build.dir/link.d CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 -[ 37%] Built target hhviterbialgorithm_with_celloff /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a -/usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[ 38%] Built target ffindex_from_fasta_with_split +[ 38%] Built target ffindex_order +/usr/bin/cc -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/ffindex_apply.dir/link.d CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a +[ 38%] Built target ffindex_build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 37%] Built target A3M_COMPRESS -[ 37%] Built target hhviterbialgorithm_with_celloff_and_ss +[ 38%] Built target A3M_COMPRESS +[ 38%] Built target ffindex_apply make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/depend make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/depend make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/depend make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_extract-plain.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_reduce-plain.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/a3m_database_filter-plain.dir/build.make src/CMakeFiles/a3m_database_filter-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_reduce-plain.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_reduce-plain.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_extract-plain.dir/DependInfo.cmake "--color=" @@ -4810,72 +4854,64 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/a3m_database_filter-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/build -make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/build -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/build +make -f src/CMakeFiles/a3m_extract-plain.dir/build.make src/CMakeFiles/a3m_extract-plain.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f src/CMakeFiles/a3m_database_reduce-plain.dir/build.make src/CMakeFiles/a3m_database_reduce-plain.dir/build make -f src/CMakeFiles/a3m_reduce-plain.dir/build.make src/CMakeFiles/a3m_reduce-plain.dir/build +make -f src/CMakeFiles/a3m_database_extract-plain.dir/build.make src/CMakeFiles/a3m_database_extract-plain.dir/build make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make -f src/CMakeFiles/a3m_database_filter-plain.dir/build.make src/CMakeFiles/a3m_database_filter-plain.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 38%] Building CXX object src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -[ 39%] Building CXX object src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[ 43%] Building CXX object src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o +[ 43%] Building CXX object src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o +[ 41%] Building CXX object src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o +[ 43%] Building CXX object src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o +[ 43%] Building CXX object src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract-plain.dir/a3m_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_extract.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce-plain.dir/a3m_database_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -[ 40%] Building CXX object src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter-plain.dir/a3m_database_filter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -[ 41%] Building CXX object src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_reduce.cpp -[ 42%] Building CXX object src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract-plain.dir/a3m_database_extract.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -[ 43%] Linking CXX static library libhhviterbialgorithm_and_ss.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp -[ 44%] Linking CXX static library libCS_OBJECTS.a -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/cs && /usr/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h > /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.crf.h.tmp -/usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -/usr/bin/ranlib libhhviterbialgorithm_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[ 46%] Linking CXX executable a3m_extract-plain -[ 46%] Linking CXX executable a3m_reduce-plain -[ 47%] Linking CXX executable a3m_database_extract-plain -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract-plain.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce-plain.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-plain.dir/link.txt --verbose=1 -[ 47%] Built target hhviterbialgorithm_and_ss cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated/context_data.lib.h.tmp 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47%] Linking CXX executable a3m_database_extract-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract-plain.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/a3m_reduce-plain.dir/link.d "CMakeFiles/a3m_reduce-plain.dir/a3m_reduce.cpp.o" -o a3m_reduce-plain ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP 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/usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhsearch.cpp +[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o +[ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhit.cpp +[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o +[ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP 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-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp +[ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhmatrices.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o.d -o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/util.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/util.cpp +[ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o +[ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd 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-I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhforwardalgorithm.cpp +[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o +[ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o +[ 72%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o +[ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o +[ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o +[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmm.cpp +[ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o +[ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriordecoderrunner.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhfullalignment.cpp -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhhmmsimd.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhposteriormatrix.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbi.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbacktracemac.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhmacalgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhprefilter.cpp +[ 78%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhviterbimatrix.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/hhbackwardalgorithm.cpp cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -MF CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o.d -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /build/reproducible-path/hhsuite-3.3.0+ds/src/ffindexdatabase.cpp @@ -4987,18 +5023,18 @@ make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhfilter-plain.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/cstranslate-plain.dir/build.make src/CMakeFiles/cstranslate-plain.dir/depend +make -f src/CMakeFiles/hhblits_omp-plain.dir/build.make src/CMakeFiles/hhblits_omp-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhsearch-plain.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_omp-plain.dir/build.make src/CMakeFiles/hhblits_omp-plain.dir/depend +make -f src/CMakeFiles/hhsearch_omp-plain.dir/build.make src/CMakeFiles/hhsearch_omp-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhalign-plain.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhsearch_omp-plain.dir/build.make src/CMakeFiles/hhsearch_omp-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhconsensus-plain.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/hhalign_omp-plain.dir/build.make src/CMakeFiles/hhalign_omp-plain.dir/depend +make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/cstranslate-plain.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/hhblits_ca3m-plain.dir/build.make src/CMakeFiles/hhblits_ca3m-plain.dir/depend make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_omp-plain.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' @@ -5009,59 +5045,61 @@ cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hhsuite-3.3.0+ds /build/reproducible-path/hhsuite-3.3.0+ds/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/CMakeFiles/hhblits_ca3m-plain.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +make -f src/CMakeFiles/hhalign-plain.dir/build.make src/CMakeFiles/hhalign-plain.dir/build make[4]: Leaving directory 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src/CMakeFiles/hhconsensus-plain.dir/hhconsensus.cpp.o +[ 83%] Building CXX object src/CMakeFiles/hhblits-plain.dir/hhblits_app.cpp.o cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/c++ -DOPENMP -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/generated -I/build/reproducible-path/hhsuite-3.3.0+ds/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simde -I/build/reproducible-path/hhsuite-3.3.0+ds/lib/simd -I/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src -I/build/reproducible-path/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhmake-plain.dir/hhmake.cpp.o -MF 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/build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp +[ 91%] Linking CXX executable hhalign-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-plain.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:49: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 24 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -5088,6 +5126,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +[ 92%] Linking CXX executable hhblits-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-plain.dir/link.txt --verbose=1 +[ 93%] Linking CXX executable hhsearch-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-plain.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -5142,14 +5184,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 92%] Linking CXX executable hhblits-plain -[ 93%] Linking CXX executable hhalign-plain -[ 93%] Linking CXX executable hhsearch-plain -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits-plain.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign-plain.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch-plain.dir/link.txt --verbose=1 -[ 94%] Linking CXX executable hhblits_ca3m-plain -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-plain.dir/link.txt --verbose=1 /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/reproducible-path/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:51: warning: '.ffindex' directive output may be truncated writing 8 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 26 | snprintf(index_filename, FILENAME_MAX, "%s.ffindex", base); @@ -5177,48 +5211,50 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable hhfilter-plain -[ 96%] Linking CXX executable hhmake-plain -[ 98%] 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libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[ 94%] Linking CXX executable hhblits_ca3m-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m-plain.dir/link.txt --verbose=1 +[ 94%] Built target hhalign-plain +[ 95%] Linking CXX executable hhalign_omp-plain cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp-plain.dir/link.txt --verbose=1 -cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-plain.dir/link.txt --verbose=1 -[ 99%] Linking CXX executable hhsearch_omp-plain +[ 96%] Linking CXX executable hhsearch_omp-plain cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits-plain.dir/link.d "CMakeFiles/hhblits-plain.dir/hhblits_app.cpp.o" -o hhblits-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP 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-std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_ca3m-plain.dir/link.d "CMakeFiles/hhblits_ca3m-plain.dir/hhblits_ca3m.cpp.o" -o hhblits_ca3m-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-plain.dir/link.d "CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o" -o hhsearch_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhalign_omp-plain.dir/link.d "CMakeFiles/hhalign_omp-plain.dir/hhblits_omp.cpp.o" -o hhalign_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhsearch_omp-plain.dir/link.d "CMakeFiles/hhsearch_omp-plain.dir/hhblits_omp.cpp.o" -o hhsearch_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[ 97%] Built target hhblits_ca3m-plain +[ 97%] Built target hhsearch_omp-plain +[ 97%] Built target hhalign_omp-plain +[100%] Linking CXX executable hhmake-plain +[100%] Linking CXX executable hhfilter-plain +[100%] Linking CXX executable hhconsensus-plain +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter-plain.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake-plain.dir/link.txt --verbose=1 +cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus-plain.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-plain.dir/link.d "CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o" -o hhblits_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +[100%] Built target hhblits_omp-plain +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhfilter-plain.dir/link.d "CMakeFiles/hhfilter-plain.dir/hhfilter.cpp.o" -o hhfilter-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[100%] Built target hhalign_omp-plain -[100%] Built target hhsearch_omp-plain [100%] Built target hhfilter-plain +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhconsensus-plain.dir/link.d "CMakeFiles/hhconsensus-plain.dir/hhconsensus.cpp.o" -o hhconsensus-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhmake-plain.dir/link.d "CMakeFiles/hhmake-plain.dir/hhmake.cpp.o" -o hhmake-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a +make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' [100%] Built target hhconsensus-plain [100%] Built target hhmake-plain -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hhblits_omp-plain.dir/link.d "CMakeFiles/hhblits_omp-plain.dir/hhblits_omp.cpp.o" -o hhblits_omp-plain libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a -make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' -[100%] Built target hhblits_omp-plain [100%] Linking CXX executable cstranslate-plain cd /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate-plain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hhsuite-3.3.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -mfpmath=sse -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/cstranslate-plain.dir/link.d "CMakeFiles/cstranslate-plain.dir/cs/cstranslate_app.cc.o" -o cstranslate-plain libHH_OBJECTS.a libA3M_COMPRESS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a @@ -5231,7 +5267,7 @@ debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_build --builddirectory mybuild/data - cd mybuild/data && make -j42 "INSTALL=install --strip-program=true" + cd mybuild/data && make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/CMakeFiles /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data//CMakeFiles/progress.marks @@ -5243,15 +5279,15 @@ make[4]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build make[4]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild' -[ 33%] Generating ../generated/context_data.crf.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -[100%] Generating ../generated/context_data.lib.h [100%] Generating ../generated/cs219.lib.h -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +[ 66%] Generating ../generated/context_data.crf.h +[100%] Generating ../generated/context_data.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated -cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mkdir -p /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.crf > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h +cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /build/reproducible-path/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp cd /build/reproducible-path/hhsuite-3.3.0+ds/data && mv -f /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h cd /build/reproducible-path/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/reproducible-path/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp @@ -5272,179 +5308,179 @@ for file in *-plain ; \ do ln -s /build/reproducible-path/hhsuite-3.3.0+ds/build_plain/src/${file} /build/reproducible-path/hhsuite-3.3.0+ds/debian/testdir/${file%%-plain} ; done cd /build/reproducible-path/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/reproducible-path/hhsuite-3.3.0+ds/build_plain/lib/ffindex/src/:/build/reproducible-path/hhsuite-3.3.0+ds/debian/testdir ./test.sh -- 12:14:31.314 INFO: query.a3m is in A2M, A3M or FASTA format +- 06:01:54.482 INFO: query.a3m is in A2M, A3M or FASTA format -- 12:14:32.345 INFO: Alternative alignment: 0 +- 06:01:54.857 INFO: Alternative alignment: 0 -- 12:14:32.372 INFO: 1 alignments done +- 06:01:54.864 INFO: 1 alignments done -- 12:14:32.407 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm +- 06:01:54.885 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29221 Searched_HMMs 1 -Date Tue Oct 13 12:14:32 2026 +Date Wed Sep 10 06:01:54 2025 Command hhalign -i query.a3m -o result.hhr -t query.a3m No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 9E-168 9E-168 1246.9 0.0 431 1-431 1-431 (431) -query.a3m 0 32127 271 0 -query.a3m 0 32666 6 0 -query.a3m 0 32666 219 0 +query.a3m 0 32127 119 0 +query.a3m 0 32666 3 0 +query.a3m 0 32666 77 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... -- 12:14:35.367 INFO: Searching 1 column state sequences. +- 06:01:55.751 INFO: Searching 1 column state sequences. -- 12:14:35.515 INFO: query.a3m is in A2M, A3M or FASTA format +- 06:01:55.808 INFO: query.a3m is in A2M, A3M or FASTA format -- 12:14:35.539 INFO: Iteration 1 +- 06:01:55.825 INFO: Iteration 1 -- 12:14:36.101 INFO: Prefiltering database +- 06:01:56.110 INFO: Prefiltering database -- 12:14:36.924 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 06:01:56.394 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 12:14:36.925 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 06:01:56.394 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 12:14:36.925 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 06:01:56.394 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 12:14:36.925 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 06:01:56.394 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 12:14:37.070 INFO: Alternative alignment: 0 +- 06:01:56.450 INFO: Alternative alignment: 0 -- 12:14:37.081 INFO: 1 alignments done +- 06:01:56.456 INFO: 1 alignments done -- 12:14:37.081 INFO: Alternative alignment: 1 +- 06:01:56.456 INFO: Alternative alignment: 1 -- 12:14:37.099 INFO: 1 alignments done +- 06:01:56.464 INFO: 1 alignments done -- 12:14:37.100 INFO: Alternative alignment: 2 +- 06:01:56.464 INFO: Alternative alignment: 2 -- 12:14:37.100 INFO: Alternative alignment: 3 +- 06:01:56.464 INFO: Alternative alignment: 3 -- 12:14:37.815 INFO: Premerge done +- 06:01:56.822 INFO: Premerge done -- 12:14:37.816 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 06:01:56.822 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 12:14:37.857 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 06:01:56.848 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 59 out of 118 Neff 4.2743 Searched_HMMs 1 -Date Tue Oct 13 12:14:37 2026 +Date Wed Sep 10 06:01:56 2025 Command hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 1E-167 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 8.3 0.38 16.3 0.0 17 78-97 344-360 (431) -- 12:14:37.913 INFO: Searching 1 column state sequences. +- 06:01:56.978 INFO: Searching 1 column state sequences. -- 12:14:38.016 INFO: Thread 0 query.a3m +- 06:01:57.024 INFO: Thread 0 query.a3m -- 12:14:38.045 INFO: query.a3m is in A2M, A3M or FASTA format +- 06:01:57.040 INFO: query.a3m is in A2M, A3M or FASTA format -- 12:14:38.086 INFO: Iteration 1 +- 06:01:57.057 INFO: Iteration 1 -- 12:14:39.117 INFO: Prefiltering database +- 06:01:57.604 INFO: Prefiltering database -- 12:14:40.030 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 06:01:58.148 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 12:14:40.030 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 06:01:58.148 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 12:14:40.030 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 06:01:58.148 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 12:14:40.030 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 06:01:58.148 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 12:14:40.081 INFO: Alternative alignment: 0 +- 06:01:58.173 INFO: Alternative alignment: 0 -- 12:14:40.091 INFO: 1 alignments done +- 06:01:58.179 INFO: 1 alignments done -- 12:14:40.091 INFO: Alternative alignment: 1 +- 06:01:58.179 INFO: Alternative alignment: 1 -- 12:14:40.102 INFO: 1 alignments done +- 06:01:58.185 INFO: 1 alignments done -- 12:14:40.102 INFO: Alternative alignment: 2 +- 06:01:58.185 INFO: Alternative alignment: 2 -- 12:14:40.102 INFO: Alternative alignment: 3 +- 06:01:58.185 INFO: Alternative alignment: 3 -- 12:14:40.967 INFO: Premerge done +- 06:01:58.761 INFO: Premerge done -- 12:14:40.968 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 06:01:58.761 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 12:14:41.007 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 06:01:58.782 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 -- 12:14:41.141 INFO: query.a3m is in A2M, A3M or FASTA format +- 06:01:58.865 INFO: query.a3m is in A2M, A3M or FASTA format -- 12:14:41.165 INFO: Searching 1 database HHMs without prefiltering +- 06:01:58.881 INFO: Searching 1 database HHMs without prefiltering -- 12:14:41.165 INFO: Iteration 1 +- 06:01:58.881 INFO: Iteration 1 -- 12:14:41.621 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 06:01:59.173 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 12:14:41.716 INFO: Alternative alignment: 0 +- 06:01:59.235 INFO: Alternative alignment: 0 -- 12:14:41.726 INFO: 1 alignments done +- 06:01:59.242 INFO: 1 alignments done -- 12:14:41.726 INFO: Alternative alignment: 1 +- 06:01:59.242 INFO: Alternative alignment: 1 -- 12:14:41.740 INFO: 1 alignments done +- 06:01:59.249 INFO: 1 alignments done -- 12:14:41.740 INFO: Alternative alignment: 2 +- 06:01:59.249 INFO: Alternative alignment: 2 -- 12:14:41.740 INFO: Alternative alignment: 3 +- 06:01:59.249 INFO: Alternative alignment: 3 -- 12:14:42.184 INFO: Premerge done +- 06:01:59.582 INFO: Premerge done -- 12:14:42.185 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 06:01:59.583 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 12:14:42.241 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 06:01:59.611 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 Match_columns 431 No_of_seqs 49 out of 118 Neff 4.29221 Searched_HMMs 1 -Date Tue Oct 13 12:14:42 2026 +Date Wed Sep 10 06:01:59 2025 Command hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 sp|Q5VUD6|FA69B_HUMAN Protein 100.0 5E-169 5E-169 1249.5 0.0 431 1-431 1-431 (431) 2 sp|Q5VUD6|FA69B_HUMAN Protein 0.2 0.38 0.38 16.3 0.0 17 78-97 344-360 (431) -- 12:14:42.331 INFO: Thread 1 query.a3m +- 06:01:59.683 INFO: Thread 0 query.a3m -- 12:14:42.351 INFO: query.a3m is in A2M, A3M or FASTA format +- 06:01:59.699 INFO: query.a3m is in A2M, A3M or FASTA format -- 12:14:42.368 INFO: Searching 1 database HHMs without prefiltering +- 06:01:59.716 INFO: Searching 1 database HHMs without prefiltering -- 12:14:42.368 INFO: Iteration 1 +- 06:01:59.716 INFO: Iteration 1 -- 12:14:43.552 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 06:02:00.263 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 12:14:43.592 INFO: Alternative alignment: 0 +- 06:02:00.294 INFO: Alternative alignment: 0 -- 12:14:43.598 INFO: 1 alignments done +- 06:02:00.301 INFO: 1 alignments done -- 12:14:43.598 INFO: Alternative alignment: 1 +- 06:02:00.301 INFO: Alternative alignment: 1 -- 12:14:43.605 INFO: 1 alignments done +- 06:02:00.307 INFO: 1 alignments done -- 12:14:43.605 INFO: Alternative alignment: 2 +- 06:02:00.307 INFO: Alternative alignment: 2 -- 12:14:43.605 INFO: Alternative alignment: 3 +- 06:02:00.307 INFO: Alternative alignment: 3 -- 12:14:44.200 INFO: Premerge done +- 06:02:00.885 INFO: Premerge done -- 12:14:44.200 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 06:02:00.885 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 12:14:44.221 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 06:02:00.906 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp @@ -5455,7 +5491,7 @@ for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \ dh_auto_install --builddirectory build_${SIMD} ; \ done - cd build_avx2 && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_avx2 && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5520,7 +5556,7 @@ -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx2' - cd build_avx && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_avx && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_avx --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5585,7 +5621,7 @@ -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_avx' - cd build_sse4.1 && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_sse4.1 && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5650,7 +5686,7 @@ -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse4.1' - cd build_ssse3 && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_ssse3 && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5715,7 +5751,7 @@ -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_ssse3' - cd build_sse3 && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_sse3 && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3 --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5780,7 +5816,7 @@ -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/renumberpdb.pl -- Up-to-date: /build/reproducible-path/hhsuite-3.3.0+ds/debian/tmp/usr/scripts/splitfasta.pl make[2]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_sse3' - cd build_plain && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build_plain && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/build_plain' /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/build_plain --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -5859,7 +5895,7 @@ debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_auto_install --builddirectory mybuild/data - cd mybuild/data && make -j42 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd mybuild/data && make -j40 install DESTDIR=/build/reproducible-path/hhsuite-3.3.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/hhsuite-3.3.0+ds/mybuild/data' cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -S/build/reproducible-path/hhsuite-3.3.0+ds -B/build/reproducible-path/hhsuite-3.3.0+ds/mybuild --check-build-system CMakeFiles/Makefile.cmake 0 cd /build/reproducible-path/hhsuite-3.3.0+ds/mybuild && make -f CMakeFiles/Makefile2 data/preinstall @@ -5916,8 +5952,8 @@ make[1]: Leaving directory '/build/reproducible-path/hhsuite-3.3.0+ds' dh_md5sums dh_builddeb -dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_amd64.deb'. dpkg-deb: building package 'hhsuite' in '../hhsuite_3.3.0+ds-8_amd64.deb'. +dpkg-deb: building package 'hhsuite-dbgsym' in '../hhsuite-dbgsym_3.3.0+ds-8_amd64.deb'. dpkg-deb: building package 'hhsuite-data' in '../hhsuite-data_3.3.0+ds-8_all.deb'. dpkg-genbuildinfo --build=binary -O../hhsuite_3.3.0+ds-8_amd64.buildinfo dpkg-genchanges --build=binary -O../hhsuite_3.3.0+ds-8_amd64.changes @@ -5926,12 +5962,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3897769/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3897769/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/3607408 and its subdirectories -I: Current time: Tue Oct 13 00:18:37 -12 2026 -I: pbuilder-time-stamp: 1791893917 +I: removing directory /srv/workspace/pbuilder/3897769 and its subdirectories +I: Current time: Wed Sep 10 20:05:04 +14 2025 +I: pbuilder-time-stamp: 1757484304