Diff of the two buildlogs: -- --- b1/build.log 2023-04-12 11:33:51.569442522 +0000 +++ b2/build.log 2023-04-12 11:42:16.083686689 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 11 23:27:05 -12 2023 -I: pbuilder-time-stamp: 1681298825 +I: Current time: Wed May 15 07:56:58 +14 2024 +I: pbuilder-time-stamp: 1715709418 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./hhsuite_3.3.0+ds.orig.tar.xz] I: copying [./hhsuite_3.3.0+ds-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Oct 25 01:36:26 2022 -12 +gpgv: Signature made Wed Oct 26 03:36:26 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hhsuite_3.3.0+ds-7.dsc: no acceptable signature found @@ -33,11 +33,20 @@ dpkg-source: info: applying exe_suffix I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4432/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/9255/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' @@ -47,38 +56,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='4432' + PPID='9255' PS1='# ' PS2='> ' 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.WYgoK1Vc/pbuilderrc_GDFr --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WYgoK1Vc/b1 --logfile b1/build.log hhsuite_3.3.0+ds-7.dsc' + 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.WYgoK1Vc/pbuilderrc_Lb4f --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WYgoK1Vc/b2 --logfile b2/build.log --extrapackages usrmerge hhsuite_3.3.0+ds-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4432/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 15 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/9255/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -211,7 +220,7 @@ Get: 87 http://deb.debian.org/debian bookworm/main arm64 imagemagick-6.q16 arm64 8:6.9.11.60+dfsg-1.6 [339 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 imagemagick arm64 8:6.9.11.60+dfsg-1.6 [122 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libsimde-dev all 0.7.4~rc2-2 [377 kB] -Fetched 43.0 MB in 1s (51.1 MB/s) +Fetched 43.0 MB in 1s (43.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19616 files and directories currently installed.) @@ -604,8 +613,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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-7_source.changes +I: user script /srv/workspace/pbuilder/9255/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/9255/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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-7_source.changes dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.3.0+ds-7 dpkg-buildpackage: info: source distribution unstable @@ -700,61 +718,60 @@ make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/data /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/data /build/hhsuite-3.3.0+ds/mybuild/data/CMakeFiles/generated.dir/DependInfo.cmake --color= 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[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --color= -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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --color= +make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src/cs /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src/cs /build/hhsuite-3.3.0+ds/mybuild/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --color= -make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build +make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build +make -f 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src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build -[ 1%] Generating ../generated/context_data.crf.h make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build +[ 1%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 2%] Generating ../generated/context_data.crf.h +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd 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/build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -[ 3%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -[ 4%] Generating ../generated/context_data.lib.h -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex.c -cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/a3m_compress.cpp -[ 5%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/aa.cc -cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h -[ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o +[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 7%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhviterbialgorithm.cpp -[ 8%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffutil.c +[ 7%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/a3m_compress.cpp +[ 8%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/as.cc [ 9%] Linking C static library libffindex.a cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 @@ -805,90 +822,99 @@ make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' [ 12%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_reduce.c -[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/as.cc -[ 14%] Linking C executable ffindex_reduce +[ 13%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc +[ 14%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc +[ 15%] Linking C executable ffindex_reduce cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 14%] Built target ffindex_reduce +[ 15%] Built target ffindex_reduce make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o +[ 16%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_build.c -[ 16%] Linking C executable ffindex_build +[ 17%] Linking C executable ffindex_build cd /build/hhsuite-3.3.0+ds/mybuild/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 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 16%] Built target ffindex_build +[ 17%] Built target ffindex_build 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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src 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char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp -cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +[ 19%] Linking C executable ffindex_from_fasta +cd /build/hhsuite-3.3.0+ds/mybuild/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 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 19%] Built target ffindex_from_fasta make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake --color= -[ 19%] Linking C executable ffindex_from_fasta -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o ffindex_from_fasta libffindex.a [ 20%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_get.c +[ 21%] Linking CXX static library libA3M_COMPRESS.a +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake +[ 22%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +cd /build/hhsuite-3.3.0+ds/mybuild/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/hhsuite-3.3.0+ds/mybuild' -[ 20%] Built target ffindex_from_fasta +[ 22%] Built target A3M_COMPRESS make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o +[ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_modify.c -[ 22%] Linking C executable ffindex_get +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp +[ 24%] Linking C executable ffindex_get cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a -[ 23%] Linking C executable ffindex_modify -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 24%] Linking CXX static library libA3M_COMPRESS.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake [ 24%] Built target ffindex_get make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -/usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_unpack.c -/usr/bin/ranlib libA3M_COMPRESS.a +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +[ 26%] Linking C executable ffindex_modify +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 +[ 27%] Linking CXX static library libhhviterbialgorithm_with_celloff.a +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a +[ 28%] Generating ../generated/context_data.lib.h +cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 +cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl context_data.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 25%] Built target 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 +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 28%] Built target ffindex_modify make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake --color= -[ 25%] Built target A3M_COMPRESS +[ 28%] Built target hhviterbialgorithm_with_celloff 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/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/lib/ffindex/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src 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-Werror=format-security -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/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_order.c -[ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o +[ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cc -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/lib/ffindex/src/ext -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /build/hhsuite-3.3.0+ds/lib/ffindex/src/ffindex_from_fasta_with_split.c -[ 28%] Linking C executable ffindex_unpack +[ 31%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake +cd /build/hhsuite-3.3.0+ds/mybuild/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_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/hhsuite-3.3.0+ds/mybuild' +[ 32%] Linking C executable ffindex_unpack cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 +[ 32%] Built target hhviterbialgorithm_with_celloff_and_ss /usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 28%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --color= +[ 33%] Linking CXX static library libhhviterbialgorithm_and_ss.a +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build -[ 29%] Linking C executable ffindex_from_fasta_with_split -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 30%] Linking C executable ffindex_order -cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a -/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a -[ 31%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 +[ 34%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_extract.cpp +/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/hhsuite-3.3.0+ds/mybuild' -[ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/assert_helpers.cc -[ 32%] Built target ffindex_from_fasta_with_split make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 34%] Built target ffindex_unpack make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --color= -[ 32%] Built target ffindex_order -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 34%] Built target hhviterbialgorithm_and_ss make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --color= -[ 33%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 35%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_reduce.cpp make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 34%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o +[ 36%] Linking C executable ffindex_order +cd /build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 +[ 37%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_reduce.cpp -cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp -[ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.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/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.crf.h +/usr/bin/cc -std=c99 -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a +[ 38%] Linking C executable ffindex_from_fasta_with_split +cd /build/hhsuite-3.3.0+ds/mybuild/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 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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/hhsuite-3.3.0+ds/mybuild' -[ 35%] Built target hhviterbialgorithm_with_celloff +[ 38%] Built target ffindex_order make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --color= -[ 35%] Built target generated -make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 38%] Built target ffindex_from_fasta_with_split +make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --color= +[ 39%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 36%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_extract.cpp -[ 37%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o +[ 40%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /build/hhsuite-3.3.0+ds/src/a3m_database_filter.cpp -[ 38%] Linking CXX static library libhhviterbialgorithm_and_ss.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 -/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/hhsuite-3.3.0+ds/mybuild' -[ 38%] Built target hhviterbialgorithm_and_ss -[ 39%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/blosum_matrix.cc -[ 40%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake -cd /build/hhsuite-3.3.0+ds/mybuild/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_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/hhsuite-3.3.0+ds/mybuild' -[ 40%] Built target hhviterbialgorithm_with_celloff_and_ss -[ 41%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/getopt_pp.cc +[ 41%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/log.cc [ 42%] Linking CXX executable a3m_extract cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -[ 43%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/log.cc -[ 44%] Linking CXX executable a3m_reduce +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 42%] Built target a3m_extract +[ 43%] Linking CXX executable a3m_reduce cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 +[ 44%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o +cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/application.cc /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 45%] Linking CXX executable a3m_database_reduce cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 -[ 45%] Built target a3m_extract /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a -[ 46%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -cd /build/hhsuite-3.3.0+ds/mybuild/src/cs && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/cs/application.cc +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 45%] Built target a3m_reduce +[ 46%] Generating ../generated/cs219.lib.h +cd /build/hhsuite-3.3.0+ds/data && mkdir -p /build/hhsuite-3.3.0+ds/mybuild/generated +cd /build/hhsuite-3.3.0+ds/data && /build/hhsuite-3.3.0+ds/cmake/xxdi.pl cs219.lib > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/cs219.lib.h +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 46%] Built target a3m_database_reduce [ 47%] Linking CXX executable a3m_database_extract cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 +cd /build/hhsuite-3.3.0+ds/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h > /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 47%] Built target a3m_database_reduce -[ 47%] Built target a3m_reduce -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/data && mv -f /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h.tmp /build/hhsuite-3.3.0+ds/mybuild/generated/context_data.lib.h [ 47%] Built target a3m_database_extract +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 47%] Built target generated [ 48%] Linking CXX executable a3m_database_filter cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a @@ -1030,19 +1048,19 @@ make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.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 -[ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o +[ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhblits.cpp +[ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhdecl.cpp +[ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhhit.cpp -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o +[ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhmatrices.cpp -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/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/hhsearch.cpp.o +[ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhalign.cpp +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhsearch.cpp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhhitlist.cpp [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -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/hhsuite-3.3.0+ds/src/hhposteriordecoder.cpp @@ -1122,67 +1140,67 @@ [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend -make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend -make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend -make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake --color= -make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend -make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend +make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src 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src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o +[ 85%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -MF CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o.d -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhconsensus.cpp -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP 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CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o.d -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /build/hhsuite-3.3.0+ds/src/cs/cstranslate_app.cc [ 88%] Linking CXX executable hhalign cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 @@ -1190,16 +1208,39 @@ [ 89%] Linking CXX executable hhsearch cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch 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 +[ 90%] Linking CXX executable hhblits +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits 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/hhsuite-3.3.0+ds/mybuild' -[ 89%] Built target hhalign +[ 90%] Built target hhalign make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build -[ 90%] Linking CXX executable hhblits -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 91%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 91%] Built target hhsearch +make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend +[ 91%] Built target hhblits +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color= +make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build +make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 92%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp +[ 93%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/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); @@ -1227,53 +1268,30 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits.dir/hhblits_app.cpp.o -o hhblits 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 -[ 91%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHSEARCH=1 -MD -MT src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 91%] Built target hhsearch -make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -[ 92%] Linking CXX executable hhblits_omp +[ 94%] Linking CXX executable hhblits_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 -[ 93%] Building CXX object src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -DHHALIGN=1 -MD -MT src/CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -MF CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o.d -o CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp 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/hhsuite-3.3.0+ds/mybuild' -[ 93%] Built target hhblits -make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' -cd /build/hhsuite-3.3.0+ds/mybuild && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hhsuite-3.3.0+ds /build/hhsuite-3.3.0+ds/src /build/hhsuite-3.3.0+ds/mybuild /build/hhsuite-3.3.0+ds/mybuild/src /build/hhsuite-3.3.0+ds/mybuild/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --color= -[ 94%] Linking CXX executable hhfilter +[ 95%] Linking CXX executable hhfilter cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' -make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build -make[4]: Entering directory '/build/hhsuite-3.3.0+ds/mybuild' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp 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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhfilter.dir/hhfilter.cpp.o -o hhfilter 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%] Building CXX object src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/c++ -DOPENMP -I/build/hhsuite-3.3.0+ds/mybuild/generated -I/build/hhsuite-3.3.0+ds/src -I/build/hhsuite-3.3.0+ds/lib/ffindex/src -I/build/hhsuite-3.3.0+ds/lib/simde -I/build/hhsuite-3.3.0+ds/lib/simd -I/build/hhsuite-3.3.0+ds/mybuild/src -I/build/hhsuite-3.3.0+ds/src/cs -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -MD -MT src/CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -MF CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o.d -o CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -c /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[ 95%] Built target hhfilter [ 96%] Linking CXX executable hhmake cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhmake.dir/hhmake.cpp.o -o hhmake 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/hhsuite-3.3.0+ds/mybuild' -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 96%] Built target hhblits_omp -[ 96%] Built target hhfilter [ 97%] Linking CXX executable hhconsensus cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -o hhconsensus 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/hhsuite-3.3.0+ds/mybuild' [ 97%] Built target hhmake make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [ 97%] Built target hhconsensus -/build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': -/build/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); - | ^~~~~~~~ +/build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': +/build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -1285,11 +1303,10 @@ from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, - from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34, - from /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:8: + from /build/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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, - inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: + inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, + inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1297,10 +1314,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp: In function 'int main(int, const char**)': -/build/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/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': +/build/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:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -1312,10 +1329,11 @@ from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/hhsuite-3.3.0+ds/src/hhblits.h:11, - from /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:8: + from /build/hhsuite-3.3.0+ds/src/hhsearch.h:34, + from /build/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/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:24:15, - inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_ca3m.cpp:358:29: + inlined from 'void OutputFFIndex::close()' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:26:17, + inlined from 'int main(int, const char**)' at /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp:167:33: /usr/include/aarch64-linux-gnu/bits/stdio2.h:54:35: note: '__builtin___snprintf_chk' output between 9 and 4104 bytes into a destination of size 4096 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1323,9 +1341,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable hhsearch_omp -cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp 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 /build/hhsuite-3.3.0+ds/src/hhblits_omp.cpp: In function 'int main(int, const char**)': /build/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); @@ -1353,18 +1368,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -[ 99%] Linking CXX executable hhblits_ca3m +[ 98%] Linking CXX executable hhblits_ca3m cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits_ca3m.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m 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/hhsuite-3.3.0+ds/mybuild' -[ 99%] Built target hhsearch_omp -[100%] Linking CXX executable hhalign_omp +[ 99%] Linking CXX executable hhalign_omp cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign_omp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m 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/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhalign_omp.dir/hhblits_omp.cpp.o -o hhalign_omp 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 +[100%] Linking CXX executable hhsearch_omp +cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp 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/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhblits_ca3m make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' [100%] Built target hhalign_omp +make[4]: Leaving directory '/build/hhsuite-3.3.0+ds/mybuild' +[100%] Built target hhsearch_omp [100%] Linking CXX executable cstranslate cd /build/hhsuite-3.3.0+ds/mybuild/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hhsuite-3.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -include stdlib.h -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++0x -fsigned-char -fopenmp -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -o cstranslate 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 @@ -1399,179 +1417,179 @@ debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/hhsuite-3.3.0+ds' cd /build/hhsuite-3.3.0+ds/data && PATH=$PATH:/build/hhsuite-3.3.0+ds/mybuild/src:/build/hhsuite-3.3.0+ds/mybuild/lib/ffindex/src ./test.sh -- 23:31:31.601 INFO: query.a3m is in A2M, A3M or FASTA format +- 08:02:28.930 INFO: query.a3m is in A2M, A3M or FASTA format -- 23:31:33.104 INFO: Alternative alignment: 0 +- 08:02:30.997 INFO: Alternative alignment: 0 -- 23:31:33.143 INFO: 1 alignments done +- 08:02:31.049 INFO: 1 alignments done -- 23:31:33.264 INFO: Realigning 1 HMM-HMM alignments using Maximum Accuracy algorithm +- 08:02:31.192 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 4.29223 Searched_HMMs 1 -Date Tue Apr 11 23:31:33 2023 +Date Wed May 15 08:02:31 2024 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 685 0 -query.a3m 0 32666 5 0 -query.a3m 0 32666 248 0 +query.a3m 0 32127 1027 0 +query.a3m 0 32666 7 0 +query.a3m 0 32666 267 0 Reading context library for pseudocounts from internal ... Reading abstract state alphabet from internal ... Processing entry: query.a3m Adding cs-pseudocounts (admix=0.30) ... -- 23:31:37.684 INFO: Searching 1 column state sequences. +- 08:02:36.672 INFO: Searching 1 column state sequences. -- 23:31:37.847 INFO: query.a3m is in A2M, A3M or FASTA format +- 08:02:36.853 INFO: query.a3m is in A2M, A3M or FASTA format -- 23:31:37.912 INFO: Iteration 1 +- 08:02:36.923 INFO: Iteration 1 -- 23:31:38.958 INFO: Prefiltering database +- 08:02:38.274 INFO: Prefiltering database -- 23:31:40.011 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 08:02:39.605 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 23:31:40.011 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 08:02:39.605 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 23:31:40.011 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 08:02:39.605 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 23:31:40.012 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 08:02:39.605 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 23:31:40.180 INFO: Alternative alignment: 0 +- 08:02:39.799 INFO: Alternative alignment: 0 -- 23:31:40.215 INFO: 1 alignments done +- 08:02:39.848 INFO: 1 alignments done -- 23:31:40.215 INFO: Alternative alignment: 1 +- 08:02:39.848 INFO: Alternative alignment: 1 -- 23:31:40.248 INFO: 1 alignments done +- 08:02:39.891 INFO: 1 alignments done -- 23:31:40.248 INFO: Alternative alignment: 2 +- 08:02:39.891 INFO: Alternative alignment: 2 -- 23:31:40.248 INFO: Alternative alignment: 3 +- 08:02:39.891 INFO: Alternative alignment: 3 -- 23:31:41.593 INFO: Premerge done +- 08:02:41.513 INFO: Premerge done -- 23:31:41.593 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 08:02:41.513 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 23:31:41.725 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 08:02:41.664 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 4.27431 Searched_HMMs 1 -Date Tue Apr 11 23:31:41 2023 +Date Wed May 15 08:02:41 2024 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) -- 23:31:41.811 INFO: Searching 1 column state sequences. +- 08:02:41.773 INFO: Searching 1 column state sequences. -- 23:31:41.950 INFO: Thread 0 query.a3m +- 08:02:42.110 INFO: Thread 0 query.a3m -- 23:31:41.995 INFO: query.a3m is in A2M, A3M or FASTA format +- 08:02:42.175 INFO: query.a3m is in A2M, A3M or FASTA format -- 23:31:42.058 INFO: Iteration 1 +- 08:02:42.248 INFO: Iteration 1 -- 23:31:44.672 INFO: Prefiltering database +- 08:02:45.387 INFO: Prefiltering database -- 23:31:47.298 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 +- 08:02:48.537 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 1 -- 23:31:47.299 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 +- 08:02:48.537 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 1 -- 23:31:47.299 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 +- 08:02:48.537 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 1 -- 23:31:47.299 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 08:02:48.537 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 23:31:47.381 INFO: Alternative alignment: 0 +- 08:02:48.631 INFO: Alternative alignment: 0 -- 23:31:47.411 INFO: 1 alignments done +- 08:02:48.666 INFO: 1 alignments done -- 23:31:47.411 INFO: Alternative alignment: 1 +- 08:02:48.666 INFO: Alternative alignment: 1 -- 23:31:47.443 INFO: 1 alignments done +- 08:02:48.703 INFO: 1 alignments done -- 23:31:47.443 INFO: Alternative alignment: 2 +- 08:02:48.703 INFO: Alternative alignment: 2 -- 23:31:47.443 INFO: Alternative alignment: 3 +- 08:02:48.703 INFO: Alternative alignment: 3 -- 23:31:50.234 INFO: Premerge done +- 08:02:52.046 INFO: Premerge done -- 23:31:50.234 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 08:02:52.046 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 23:31:50.329 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 08:02:52.151 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 -- 23:31:50.564 INFO: query.a3m is in A2M, A3M or FASTA format +- 08:02:52.426 INFO: query.a3m is in A2M, A3M or FASTA format -- 23:31:50.631 INFO: Searching 1 database HHMs without prefiltering +- 08:02:52.495 INFO: Searching 1 database HHMs without prefiltering -- 23:31:50.631 INFO: Iteration 1 +- 08:02:52.495 INFO: Iteration 1 -- 23:31:51.756 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 08:02:53.794 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 23:31:51.935 INFO: Alternative alignment: 0 +- 08:02:53.995 INFO: Alternative alignment: 0 -- 23:31:51.982 INFO: 1 alignments done +- 08:02:54.042 INFO: 1 alignments done -- 23:31:51.982 INFO: Alternative alignment: 1 +- 08:02:54.042 INFO: Alternative alignment: 1 -- 23:31:52.014 INFO: 1 alignments done +- 08:02:54.077 INFO: 1 alignments done -- 23:31:52.014 INFO: Alternative alignment: 2 +- 08:02:54.077 INFO: Alternative alignment: 2 -- 23:31:52.014 INFO: Alternative alignment: 3 +- 08:02:54.077 INFO: Alternative alignment: 3 -- 23:31:53.418 INFO: Premerge done +- 08:02:55.691 INFO: Premerge done -- 23:31:53.418 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 08:02:55.691 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 23:31:53.550 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 08:02:55.839 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 4.29223 Searched_HMMs 1 -Date Tue Apr 11 23:31:53 2023 +Date Wed May 15 08:02:55 2024 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) -- 23:31:53.767 INFO: Thread 0 query.a3m +- 08:02:56.271 INFO: Thread 0 query.a3m -- 23:31:53.813 INFO: query.a3m is in A2M, A3M or FASTA format +- 08:02:56.336 INFO: query.a3m is in A2M, A3M or FASTA format -- 23:31:53.877 INFO: Searching 1 database HHMs without prefiltering +- 08:02:56.407 INFO: Searching 1 database HHMs without prefiltering -- 23:31:53.877 INFO: Iteration 1 +- 08:02:56.407 INFO: Iteration 1 -- 23:31:56.157 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment +- 08:02:59.139 INFO: Scoring 1 HMMs using HMM-HMM Viterbi alignment -- 23:31:56.249 INFO: Alternative alignment: 0 +- 08:02:59.239 INFO: Alternative alignment: 0 -- 23:31:56.293 INFO: 1 alignments done +- 08:02:59.286 INFO: 1 alignments done -- 23:31:56.293 INFO: Alternative alignment: 1 +- 08:02:59.286 INFO: Alternative alignment: 1 -- 23:31:56.346 INFO: 1 alignments done +- 08:02:59.340 INFO: 1 alignments done -- 23:31:56.346 INFO: Alternative alignment: 2 +- 08:02:59.340 INFO: Alternative alignment: 2 -- 23:31:56.346 INFO: Alternative alignment: 3 +- 08:02:59.340 INFO: Alternative alignment: 3 -- 23:31:58.807 INFO: Premerge done +- 08:03:02.249 INFO: Premerge done -- 23:31:58.808 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm +- 08:03:02.250 INFO: Realigning 2 HMM-HMM alignments using Maximum Accuracy algorithm -- 23:31:58.902 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 +- 08:03:02.352 INFO: 2 sequences belonging to 2 database HMMs found with an E-value < 0.001 make[1]: Leaving directory '/build/hhsuite-3.3.0+ds' create-stamp debian/debhelper-build-stamp @@ -1719,12 +1737,14 @@ 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/9255/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/9255/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/4432 and its subdirectories -I: Current time: Tue Apr 11 23:33:50 -12 2023 -I: pbuilder-time-stamp: 1681299230 +I: removing directory /srv/workspace/pbuilder/9255 and its subdirectories +I: Current time: Wed May 15 08:05:15 +14 2024 +I: pbuilder-time-stamp: 1715709915