Diff of the two buildlogs: -- --- b1/build.log 2024-04-10 22:24:57.785964219 +0000 +++ b2/build.log 2024-04-10 22:28:12.521664374 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 10 10:23:25 -12 2024 -I: pbuilder-time-stamp: 1712787805 +I: Current time: Thu Apr 11 12:25:16 +14 2024 +I: pbuilder-time-stamp: 1712787916 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying fix_reading_fasta.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27383/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14189/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 Apr 10 22:25 /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/14189/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14189/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='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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=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='18cbb24727714da3be23e35c1378ddec' - 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='27383' - PS1='# ' - PS2='> ' + INVOCATION_ID=e9362f1e330447a281260f5946e90915 + 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=14189 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.CNKFaiiP/pbuilderrc_ETO3 --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.CNKFaiiP/b1 --logfile b1/build.log kraken2_2.1.3-1.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.CNKFaiiP/pbuilderrc_13RV --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.CNKFaiiP/b2 --logfile b2/build.log kraken2_2.1.3-1.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 10 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/27383/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 8 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14189/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] -Fetched 19.2 MB in 0s (84.5 MB/s) +Fetched 19.2 MB in 1s (37.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19636 files and directories currently installed.) @@ -283,7 +315,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/kraken2-2.1.3/ && 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 > ../kraken2_2.1.3-1_source.changes +I: user script /srv/workspace/pbuilder/14189/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/14189/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/kraken2-2.1.3/ && 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 > ../kraken2_2.1.3-1_source.changes dpkg-buildpackage: info: source package kraken2 dpkg-buildpackage: info: source version 2.1.3-1 dpkg-buildpackage: info: source distribution unstable @@ -293,7 +329,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j3 clean + cd src && make -j4 clean make[1]: Entering directory '/build/reproducible-path/kraken2-2.1.3/src' rm -f *.o estimate_capacity build_db classify dump_table lookup_accession_numbers k2mask make[1]: Leaving directory '/build/reproducible-path/kraken2-2.1.3/src' @@ -305,11 +341,13 @@ dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src - cd src && make -j3 "INSTALL=install --strip-program=true" + cd src && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kraken2-2.1.3/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o estimate_capacity.o estimate_capacity.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqreader.o seqreader.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mmscanner.o mmscanner.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o omp_hack.o omp_hack.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utilities.o utilities.cc In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/queue:63, from kraken2_headers.h:15, @@ -325,12 +363,12 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o omp_hack.o omp_hack.cc -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utilities.o utilities.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build_db.o build_db.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mmap_file.o mmap_file.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compact_hash.o compact_hash.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o taxonomy.o taxonomy.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reports.o reports.cc In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from kraken2_headers.h:1, @@ -352,40 +390,6 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.cc -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/queue:63, - from kraken2_headers.h:15: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -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++/13/bits/stl_algo.h:4861:18, - inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:361:11: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __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++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:361:11: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:360:37: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from kraken2_headers.h:14, from mmap_file.h:10, @@ -447,7 +451,51 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reports.o reports.cc +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/queue:63, + from kraken2_headers.h:15: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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++/13/bits/stl_algo.h:4861:18, + inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:361:11: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __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++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:361:11: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from '_Z15ProcessSequenceRK7OptionsRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEyRN7kraken216CompactHashTableERKNSA_8TaxonomyE._omp_fn.1' at build_db.cc:360:37: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from kraken2_headers.h:1, + from classify.cc:7: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_val >]': +/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 135 | __push_heap(_RandomAccessIterator __first, + | ^~~~~~~~~~~ +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/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++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -542,28 +590,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from kraken2_headers.h:1, - from classify.cc:7: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_val >]': -/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 135 | __push_heap(_RandomAccessIterator __first, - | ^~~~~~~~~~~ -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = OutputData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hyperloglogplus.o hyperloglogplus.cc -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/queue:63, - from kraken2_headers.h:15: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OutputData&}; _Tp = OutputData; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In file included from /usr/include/c++/13/algorithm:61, from kraken2_headers.h:1, from reports.h:12, @@ -573,22 +599,6 @@ 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:564:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:567:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:570:21: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >&):: >]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -622,6 +632,13 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/queue:63, + from kraken2_headers.h:15: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, @@ -631,12 +648,7 @@ /usr/include/c++/13/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, | ^~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OutputData; _Alloc = std::allocator]', - inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = OutputData; _Sequence = std::vector; _Compare = ProcessFiles(const char*, const char*, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, OutputStreamData&, kraken2::taxon_counters_t&)::]' at /usr/include/c++/13/bits/stl_queue.h:740:13, - inlined from '_Z12ProcessFilesPKcS0_PN7kraken213KeyValueStoreERNS1_8TaxonomyERNS1_12IndexOptionsER7OptionsR19ClassificationStatsR16OutputStreamDataRSt13unordered_mapIyNS1_10ReadCountsI20HyperLogLogPlusMinusIyEEESt4hashIyESt8equal_toIyESaISt4pairIKySI_EEE._omp_fn.0' at classify.cc:373:26: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hyperloglogplus.o hyperloglogplus.cc /usr/include/c++/13/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++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -645,6 +657,8 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const OutputData&}; _Tp = OutputData; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | __final_insertion_sort(_RandomAccessIterator __first, @@ -656,15 +670,7 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66, - from /usr/include/c++/13/queue:63, - from kraken2_headers.h:15, - from hyperloglogplus.h:16, - from hyperloglogplus.cc:8: -/usr/include/c++/13/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 675 | vector(initializer_list __l, - | ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o aa_translate.o aa_translate.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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14: @@ -678,6 +684,84 @@ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:564:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:567:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'kraken2::taxid_t ClassifySequence(kraken2::Sequence&, kraken2::Sequence&, std::ostringstream&, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, kraken2::MinimizerScanner&, std::vector&, kraken2::taxon_counts_t&, std::vector >&, kraken2::taxon_counters_t&)' at classify.cc:570:21: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, + inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1950 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, + inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1950 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, + inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, + inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1950 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = OutputData; _Alloc = std::allocator]', + inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = OutputData; _Sequence = std::vector; _Compare = ProcessFiles(const char*, const char*, kraken2::KeyValueStore*, kraken2::Taxonomy&, kraken2::IndexOptions&, Options&, ClassificationStats&, OutputStreamData&, kraken2::taxon_counters_t&)::]' at /usr/include/c++/13/bits/stl_queue.h:740:13, + inlined from '_Z12ProcessFilesPKcS0_PN7kraken213KeyValueStoreERNS1_8TaxonomyERNS1_12IndexOptionsER7OptionsR19ClassificationStatsR16OutputStreamDataRSt13unordered_mapIyNS1_10ReadCountsI20HyperLogLogPlusMinusIyEEESt4hashIyESt8equal_toIyESaISt4pairIKySI_EEE._omp_fn.0' at classify.cc:373:26: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dump_table.o dump_table.cc +In file included from /usr/include/c++/13/vector:66, + from /usr/include/c++/13/queue:63, + from kraken2_headers.h:15, + from hyperloglogplus.h:16, + from hyperloglogplus.cc:8: +/usr/include/c++/13/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 675 | vector(initializer_list __l, + | ^~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lookup_accession_numbers.o lookup_accession_numbers.cc In file included from hyperloglogplus.cc:20: hyperloglogplus-bias.h: In function 'void __static_initialization_and_destruction_0()': hyperloglogplus-bias.h:64:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 @@ -770,54 +854,6 @@ hyperloglogplus-bias.h:97:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 97 | }; | ^ -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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, - inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1950 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, - inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1950 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 = kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:181:14, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, - inlined from 'void kraken2::KrakenReportDFS(uint32_t, std::ofstream&, bool, bool, Taxonomy&, taxon_counters_t&, taxon_counters_t&, uint64_t, char, int, int)' at reports.cc:187:22, - inlined from 'void kraken2::ReportKrakenStyle(std::string, bool, bool, Taxonomy&, taxon_counters_t&, uint64_t, uint64_t)' at reports.cc:209:18: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1950 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o aa_translate.o aa_translate.cc -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dump_table.o dump_table.cc -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lookup_accession_numbers.o lookup_accession_numbers.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -Wdate-time -D_FORTIFY_SOURCE=2 -c -o k2mask.o k2mask.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -o estimate_capacity estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o -Wl,-z,relro -Wl,-z,now g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken2-2.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp -Wall -std=c++11 -O3 -DLINEAR_PROBING -o build_db build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o -Wl,-z,relro -Wl,-z,now @@ -834,7 +870,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/kraken2-2.1.3' dh_auto_install -- KRAKEN2_DIR=/build/reproducible-path/kraken2-2.1.3/debian/kraken2/usr/lib/kraken2 - cd src && make -j3 install DESTDIR=/build/reproducible-path/kraken2-2.1.3/debian/kraken2 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" KRAKEN2_DIR=/build/reproducible-path/kraken2-2.1.3/debian/kraken2/usr/lib/kraken2 + cd src && make -j4 install DESTDIR=/build/reproducible-path/kraken2-2.1.3/debian/kraken2 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" KRAKEN2_DIR=/build/reproducible-path/kraken2-2.1.3/debian/kraken2/usr/lib/kraken2 make[2]: Entering directory '/build/reproducible-path/kraken2-2.1.3/src' cp estimate_capacity build_db classify dump_table lookup_accession_numbers k2mask "/build/reproducible-path/kraken2-2.1.3/debian/kraken2/usr/lib/kraken2/" make[2]: Leaving directory '/build/reproducible-path/kraken2-2.1.3/src' @@ -880,17 +916,17 @@ dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src +dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/k2mask contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/dump_table contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/classify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/kraken2/usr/lib/kraken2/k2mask contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dpkg-gencontrol: warning: package kraken2: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package kraken2: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'kraken2' in '../kraken2_2.1.3-1_armhf.deb'. dpkg-deb: building package 'kraken2-dbgsym' in '../kraken2-dbgsym_2.1.3-1_armhf.deb'. +dpkg-deb: building package 'kraken2' in '../kraken2_2.1.3-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../kraken2_2.1.3-1_armhf.buildinfo dpkg-genchanges --build=binary -O../kraken2_2.1.3-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -898,12 +934,14 @@ 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/14189/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14189/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/27383 and its subdirectories -I: Current time: Wed Apr 10 10:24:53 -12 2024 -I: pbuilder-time-stamp: 1712787893 +I: removing directory /srv/workspace/pbuilder/14189 and its subdirectories +I: Current time: Thu Apr 11 12:28:07 +14 2024 +I: pbuilder-time-stamp: 1712788087