Diff of the two buildlogs: -- --- b1/build.log 2025-01-20 11:18:15.992860106 +0000 +++ b2/build.log 2025-01-20 11:26:38.754288425 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 19 22:47:45 -12 2025 -I: pbuilder-time-stamp: 1737370065 +I: Current time: Tue Jan 21 01:18:46 +14 2025 +I: pbuilder-time-stamp: 1737371926 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying fix-shebang.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22728/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 20 11:19 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='d4cdcb6d95244a8785612f6a66302923' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='22728' - PS1='# ' - PS2='> ' + INVOCATION_ID=c59fc321cc204d8c8b0c693493a4a73d + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=24874 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.5kN5dKou/pbuilderrc_06dT --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5kN5dKou/b1 --logfile b1/build.log last-align_1542-1.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.5kN5dKou/pbuilderrc_24Rc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5kN5dKou/b2 --logfile b2/build.log last-align_1542-1.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/22728/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -198,7 +230,7 @@ Get: 79 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf python3-pil armhf 10.4.0-1.1 [478 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] -Fetched 32.7 MB in 2s (16.4 MB/s) +Fetched 32.7 MB in 1s (50.5 MB/s) Preconfiguring packages ... 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 ... 19569 files and directories currently installed.) @@ -486,8 +518,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 20 10:50:44 UTC 2025. -Universal Time is now: Mon Jan 20 10:50:44 UTC 2025. +Local time is now: Mon Jan 20 11:21:08 UTC 2025. +Universal Time is now: Mon Jan 20 11:21:08 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -552,7 +584,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/last-align-1542/ && 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 > ../last-align_1542-1_source.changes +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/last-align-1542/ && 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 > ../last-align_1542-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1542-1 dpkg-buildpackage: info: source distribution unstable @@ -564,7 +600,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/last-align-1542' dh_auto_clean - make -j5 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/last-align-1542' make[3]: Entering directory '/build/reproducible-path/last-align-1542/src' rm -f ../bin/lastdb ../bin/lastal ../bin/last-split ../bin/last-merge-batches ../bin/last-pair-probs *.o* */*.o* @@ -587,7 +623,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/last-align-1542' dh_auto_build - make -j5 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/last-align-1542' make[3]: Entering directory '/build/reproducible-path/last-align-1542/src' g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alphabet.o Alphabet.cc @@ -598,13 +634,13 @@ ../build/mat-inc.sh ../data/*.mat > ScoreMatrixData.hh g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o TantanMasker.o TantanMasker.cc In file included from SubsetSuffixArray.cc:3: SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’: SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow] 64 | | (size_t)c[i*5 + 4] << 32; | ~~~~~~~~~~~~~~~~~~~^~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o TantanMasker.o TantanMasker.cc In file included from SubsetSuffixArraySort.cc:6: SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’: SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow] @@ -615,8 +651,6 @@ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o cbrc_linalg.o cbrc_linalg.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_substitution_matrix_stats.o mcf_substitution_matrix_stats.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o tantan.o tantan.cc -echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Centroid.o Centroid.cc In file included from /usr/include/c++/14/vector:72, from mcf_substitution_matrix_stats.hh:23, from mcf_substitution_matrix_stats.cc:4: @@ -624,6 +658,7 @@ /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1542) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" > version.hh In file included from /usr/include/c++/14/vector:66: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void mcf::SubstitutionMatrixStats::calcUnbiased(const char*, const int* const*, unsigned int)’ at mcf_substitution_matrix_stats.cc:127:23: @@ -635,6 +670,7 @@ /usr/include/c++/14/bits/stl_vector.h:1442:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1442 | _M_fill_insert(begin() + __offset, __n, __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Centroid.o Centroid.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastalArguments.o LastalArguments.cc In file included from SubsetSuffixArraySearch.cc:3: @@ -643,15 +679,14 @@ 64 | | (size_t)c[i*5 + 4] << 32; | ~~~~~~~~~~~~~~~~~~~^~~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastal.o lastal.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alignment.o Alignment.cc In file included from last.hh:11, from lastal.cc:5: SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’: SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow] 64 | | (size_t)c[i*5 + 4] << 32; | ~~~~~~~~~~~~~~~~~~~^~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o Alignment.o Alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentPot.o AlignmentPot.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentWrite.o AlignmentWrite.cc In file included from /usr/include/c++/14/algorithm:61, from Centroid.hh:14, from Alignment.hh:8, @@ -731,8 +766,8 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc In file included from /usr/include/c++/14/algorithm:61, from Mmap.hh:12, from VectorOrMmap.hh:8, @@ -752,6 +787,7 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -762,14 +798,6 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_alignment_path_adder.o mcf_alignment_path_adder.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc -../build/gc-inc.sh ../data/gc.prt > GeneticCodeData.hh -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastEvaluer.o LastEvaluer.cc /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -779,7 +807,6 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/14/bits/stl_algo.h:1750:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -789,18 +816,17 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc /usr/include/c++/14/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = cbrc::Alignment; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPair.o SegmentPair.cc /usr/include/c++/14/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPairPot.o SegmentPairPot.cc /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -816,7 +842,6 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const cbrc::Alignment&, const cbrc::Alignment&)]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, inlined from ‘void cbrc::AlignmentPot::sort()’ at AlignmentPot.hh:28:26, @@ -871,7 +896,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from ‘void alignOneQuery(LastAligner&, cbrc::MultiSequence&, size_t, size_t, size_t, bool)’ at lastal.cc:1216:11, @@ -894,7 +918,7 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_alignment_path_adder.o mcf_alignment_path_adder.cc In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from ‘void alignOneQuery(LastAligner&, cbrc::MultiSequence&, size_t, size_t, size_t, bool)’ at lastal.cc:1216:11, @@ -937,6 +961,18 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc +../build/gc-inc.sh ../data/gc.prt > GeneticCodeData.hh +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastEvaluer.o LastEvaluer.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPair.o SegmentPair.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o SegmentPairPot.o SegmentPairPot.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last_split_options.o split/last_split_options.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/mcf_last_splitter.o split/mcf_last_splitter.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp @@ -980,6 +1016,20 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 +In file included from /usr/include/c++/14/bits/stl_algo.h:61, + from /usr/include/c++/14/algorithm:61, + from alp/sls_alp_regression.hpp:46, + from alp/sls_alp_data.hpp:62, + from alp/sls_alp_data.cpp:36: +/usr/include/c++/14/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: +/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1770 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from ‘static double Sls::alp_reg::median(long int, double*)’ at alp/sls_alp_regression.cpp:643:6: @@ -1020,6 +1070,14 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, inlined from ‘static void Sls::alp_reg::find_tetta_general(double (*)(double, void*), void*, double, double, long int, double, std::vector&)’ at alp/sls_alp_regression.cpp:109:6: @@ -1040,28 +1098,6 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algo.h:61, - from /usr/include/c++/14/algorithm:61, - from alp/sls_alp_regression.hpp:46, - from alp/sls_alp_data.hpp:62, - from alp/sls_alp_data.cpp:36: -/usr/include/c++/14/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: -/usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1770 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_alp.o alp/sls_alp.cpp In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, @@ -1098,10 +1134,6 @@ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split-main.o split/last-split-main.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split.o split/last-split.cc -cc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs.o last-pair-probs.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from alp/sls_alp_regression.hpp:46, @@ -1124,6 +1156,9 @@ /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o split/last-split.o split/last-split.cc +cc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs.o last-pair-probs.cc In file included from /usr/include/c++/14/vector:72, from alp/sls_fsa1_utils.hpp:40, from alp/sls_fsa1_utils.cpp:36: @@ -1142,7 +1177,46 @@ /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc +In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from ‘static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)’ at alp/sls_fsa1.cpp:10745:6: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from ‘static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)’ at alp/sls_fsa1.cpp:10745:6: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from ‘static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)’ at alp/sls_fsa1.cpp:10819:6: +/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1905 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1906 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1907 | __comp); + | ~~~~~~~ +In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/14/bits/stl_algo.h:1908:31, + inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from ‘static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)’ at alp/sls_fsa1.cpp:10819:6: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:61, from last-pair-probs.cc:9: /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: @@ -1244,7 +1318,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2479 | __len1 - __len11, __len2 - __len22, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o ScoreMatrix.o ScoreMatrix.cc /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__merge_adaptive_resize(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/14/bits/stl_algo.h:2382:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2382 | __merge_adaptive_resize(_BidirectionalIterator __first, @@ -1644,46 +1717,8 @@ | ~~~~~~~~~~~~~~~~~~ 2757 | __comp); | ~~~~~~~ -In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from ‘static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)’ at alp/sls_fsa1.cpp:10745:6: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from ‘static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)’ at alp/sls_fsa1.cpp:10745:6: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from ‘static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)’ at alp/sls_fsa1.cpp:10819:6: -/usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1905 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1906 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1907 | __comp); - | ~~~~~~~ -In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/14/bits/stl_algo.h:1908:31, - inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from ‘static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)’ at alp/sls_fsa1.cpp:10819:6: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc In function ‘void std::__stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::stable_sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4994:36, inlined from ‘void parseBatch(const char* const*, const char* const*, char, double, const std::set >&, std::vector&)’ at last-pair-probs.cc:537:14: @@ -1715,15 +1750,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4959 | _DistanceType(__buf.size()), __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o lastdb.o lastdb.cc -g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GeneticCode.o GeneticCode.cc In file included from last.hh:11, from lastdb.cc:6: SubsetSuffixArray.hh: In function ‘size_t cbrc::getItem(mcf::ConstPackedArray, size_t)’: SubsetSuffixArray.hh:64:29: warning: left shift count >= width of type [-Wshift-count-overflow] 64 | | (size_t)c[i*5 + 4] << 32; | ~~~~~~~~~~~~~~~~~~~^~~~~ +g++ -DALPHABET_CAPACITY=66 -DHAS_CXX_THREADS -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -I. -c -o GeneticCode.o GeneticCode.cc g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-split Alphabet.o LambdaCalculator.o MultiSequence.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last_split_options.o split/last-split-main.o split/cbrc_split_aligner.o split/mcf_last_splitter.o split/last-split.o cc -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/last-align-1542=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-merge-batches last-merge-batches.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -O3 -std=c++11 -pthread -Wl,-z,relro -Wl,-z,now -pthread -o ../bin/last-pair-probs last-pair-probs.o last-pair-probs-main.o -lz @@ -1829,11 +1865,11 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged +dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/last-align-1542' @@ -1850,12 +1886,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/24874/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/24874/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/22728 and its subdirectories -I: Current time: Sun Jan 19 23:18:10 -12 2025 -I: pbuilder-time-stamp: 1737371890 +I: removing directory /srv/workspace/pbuilder/24874 and its subdirectories +I: Current time: Tue Jan 21 01:26:33 +14 2025 +I: pbuilder-time-stamp: 1737372393