Diff of the two buildlogs: -- --- b1/build.log 2025-01-17 21:28:56.158172885 +0000 +++ b2/build.log 2025-01-17 21:33:58.668448244 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 17 09:25:30 -12 2025 -I: pbuilder-time-stamp: 1737149130 +I: Current time: Sat Jan 18 11:29:34 +14 2025 +I: pbuilder-time-stamp: 1737149374 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying simde I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18809/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17794/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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 17 21:29 /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/17794/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17794/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=3 ' - DISTRIBUTION='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='08c0fe164eea41f9ac5fc5fd3016fb7f' - 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='18809' - PS1='# ' - PS2='> ' + INVOCATION_ID=a98df07232114b9ab37423651f64b8c8 + 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=17794 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.xdQL4ySU/pbuilderrc_daDV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xdQL4ySU/b1 --logfile b1/build.log last-align_1608-1.dsc' - SUDO_GID='110' - SUDO_UID='103' - 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.xdQL4ySU/pbuilderrc_rAL9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xdQL4ySU/b2 --logfile b2/build.log last-align_1608-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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 virt32z 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18809/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/17794/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -188,7 +220,7 @@ Get: 70 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf python3-pil armhf 10.4.0-1.1 [478 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] -Fetched 32.3 MB in 4s (7891 kB/s) +Fetched 32.3 MB in 1s (42.1 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 ... 19564 files and directories currently installed.) @@ -443,8 +475,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 17 21:26:14 UTC 2025. -Universal Time is now: Fri Jan 17 21:26:14 UTC 2025. +Local time is now: Fri Jan 17 21:30:17 UTC 2025. +Universal Time is now: Fri Jan 17 21:30:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -504,7 +536,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/last-align-1608/ && 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_1608-1_source.changes +I: user script /srv/workspace/pbuilder/17794/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/17794/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/last-align-1608/ && 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_1608-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1608-1 dpkg-buildpackage: info: source distribution unstable @@ -516,7 +552,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/last-align-1608' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/src' rm -f ../bin/lastdb ../bin/lastal ../bin/last-split ../bin/last-merge-batches ../bin/last-pair-probs *.o* */*.o* @@ -539,7 +575,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/last-align-1608' dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/last-align-1608' make[3]: Entering directory '/build/reproducible-path/last-align-1608/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 @@ -550,18 +586,18 @@ ../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 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] 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 TantanMasker.o TantanMasker.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 dna_words_finder.o dna_words_finder.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 fileMap.o fileMap.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 cbrc_linalg.o cbrc_linalg.cc @@ -569,6 +605,7 @@ 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: 1608) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'`\" | cmp -s version.hh - || echo \"`test -e ../.git && git describe --dirty || echo ' (HEAD -> main, tag: 1608) ' | 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 +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 In file included from /usr/include/c++/14/vector:72, from mcf_substitution_matrix_stats.hh:23, from mcf_substitution_matrix_stats.cc:4: @@ -587,21 +624,20 @@ /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 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: 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 LastalArguments.o LastalArguments.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 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 In file included from /usr/include/c++/14/algorithm:61, from Centroid.hh:14, @@ -642,15 +678,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/algorithm:61, - from Mmap.hh:12, - from VectorOrMmap.hh:8, - from MultiSequence.hh:14, - from last.hh:8: -/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_less_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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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::eraseSuboptimal()’ at AlignmentPot.cc:10:12: @@ -691,6 +718,17 @@ /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 +In file included from /usr/include/c++/14/algorithm:61, + from Mmap.hh:12, + from VectorOrMmap.hh:8, + from MultiSequence.hh:14, + from last.hh:8: +/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_less_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, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ /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, @@ -701,9 +739,10 @@ /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 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 +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 /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, @@ -812,6 +851,7 @@ /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 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::AlignmentText; _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, @@ -824,7 +864,6 @@ /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 GappedXdropAlignerPssm.o GappedXdropAlignerPssm.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::AlignmentText&, const cbrc::AlignmentText&)]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, inlined from ‘void cullFinalAlignments(std::vector&, size_t, size_t)’ at lastal.cc:971:7: @@ -853,6 +892,7 @@ /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 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:1268:11, @@ -875,6 +915,8 @@ /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 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 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:1268:11, @@ -917,12 +959,6 @@ /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 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 @@ -947,6 +983,7 @@ /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +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_data.o alp/sls_alp_data.cpp /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 /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]’: @@ -1015,7 +1052,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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_data.o alp/sls_alp_data.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, 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: @@ -1037,7 +1073,6 @@ 1822 | std::__insertion_sort(__first, __last, __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 -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_basic.o alp/sls_basic.cpp 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, @@ -1080,6 +1115,7 @@ /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++ -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_basic.o alp/sls_basic.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/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.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/njn_localmaxstat.o alp/njn_localmaxstat.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/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp @@ -1094,24 +1130,7 @@ 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 -In file included from /usr/include/c++/14/vector:72, - from alp/sls_fsa1_utils.hpp:40, - from alp/sls_fsa1_utils.cpp:36: -/usr/include/c++/14/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: -/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>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:66: -In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector >&, const std::vector&, std::vector&)’ at alp/sls_fsa1_utils.cpp:1805:13: -/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); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, - inlined from ‘static void Sls::FSA_utils::multiply_matrices(const std::vector >&, const std::vector >&, std::vector >&)’ at alp/sls_fsa1_utils.cpp:1758:17: -/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 split/last-split.o split/last-split.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, @@ -1134,49 +1153,26 @@ /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 +In file included from /usr/include/c++/14/vector:72, + from alp/sls_fsa1_utils.hpp:40, + from alp/sls_fsa1_utils.cpp:36: +/usr/include/c++/14/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: +/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>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/vector:66: +In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, + inlined from ‘static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector >&, const std::vector&, std::vector&)’ at alp/sls_fsa1_utils.cpp:1805:13: +/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); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, + inlined from ‘static void Sls::FSA_utils::multiply_matrices(const std::vector >&, const std::vector >&, std::vector >&)’ at alp/sls_fsa1_utils.cpp:1758:17: +/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); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-1608=. -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 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]’: @@ -1248,6 +1244,46 @@ | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:2359:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:2359:5: 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 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); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h: In function ‘_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]’: /usr/include/c++/14/bits/stl_algo.h:1235:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1235 | __rotate(_RandomAccessIterator __first, @@ -1375,6 +1411,7 @@ /usr/include/c++/14/bits/stl_algo.h:2748:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2748 | 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 CyclicSubsetSeed.o CyclicSubsetSeed.cc In function ‘void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘void std::__inplace_stable_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:2752:33, inlined from ‘void std::__inplace_stable_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:2752:33, @@ -1709,7 +1746,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 CyclicSubsetSeed.o CyclicSubsetSeed.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 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 @@ -1846,12 +1882,14 @@ 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/17794/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17794/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/18809 and its subdirectories -I: Current time: Fri Jan 17 09:28:52 -12 2025 -I: pbuilder-time-stamp: 1737149332 +I: removing directory /srv/workspace/pbuilder/17794 and its subdirectories +I: Current time: Sat Jan 18 11:33:53 +14 2025 +I: pbuilder-time-stamp: 1737149633