Diff of the two buildlogs: -- --- b1/build.log 2025-01-13 13:45:54.205234721 +0000 +++ b2/build.log 2025-01-13 13:52:57.377972221 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 13 01:36:24 -12 2025 -I: pbuilder-time-stamp: 1736775384 +I: Current time: Tue Jan 14 03:46:03 +14 2025 +I: pbuilder-time-stamp: 1736775963 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 reproducible_build I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/19526/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14019/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 13 13:46 /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/14019/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14019/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='ae33a71f9bd54449a376e9b3492b4bfc' - 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='19526' - PS1='# ' - PS2='> ' + INVOCATION_ID=1ec2ba73e38c4d57bc7788c4b47b3dd3 + 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=14019 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.d3cB33Dl/pbuilderrc_tC2o --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.d3cB33Dl/b1 --logfile b1/build.log ataqv_1.3.1+ds-2.dsc' - SUDO_GID='112' - SUDO_UID='106' - 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.d3cB33Dl/pbuilderrc_fb1P --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.d3cB33Dl/b2 --logfile b2/build.log ataqv_1.3.1+ds-2.dsc' + SUDO_GID=110 + SUDO_UID=103 + 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 virt32b 6.1.0-29-armmp-lpae #1 SMP Debian 6.1.123-1 (2025-01-02) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-29-arm64 #1 SMP Debian 6.1.123-1 (2025-01-02) 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/19526/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/14019/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -318,7 +350,7 @@ Get: 173 http://deb.debian.org/debian trixie/main armhf node-d3-zoom all 1.8.3+~1.8.4-1 [26.8 kB] Get: 174 http://deb.debian.org/debian trixie/main armhf node-d3 all 5.16.0+~cs5.28.10-2 [223 kB] Get: 175 http://deb.debian.org/debian trixie/main armhf node-normalize.css all 8.0.1-5 [12.7 kB] -Fetched 70.7 MB in 7s (10.9 MB/s) +Fetched 70.7 MB in 7s (10.4 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 ... 19567 files and directories currently installed.) @@ -898,8 +930,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 13 13:38:27 UTC 2025. -Universal Time is now: Mon Jan 13 13:38:27 UTC 2025. +Local time is now: Mon Jan 13 13:47:03 UTC 2025. +Universal Time is now: Mon Jan 13 13:47:03 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:armhf (1.83.0-4) ... @@ -1047,7 +1079,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ataqv-1.3.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ataqv_1.3.1+ds-2_source.changes +I: user script /srv/workspace/pbuilder/14019/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/14019/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ataqv-1.3.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ataqv_1.3.1+ds-2_source.changes dpkg-buildpackage: info: source package ataqv dpkg-buildpackage: info: source version 1.3.1+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -1057,7 +1093,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.1+ds' make[1]: Leaving directory '/build/reproducible-path/ataqv-1.3.1+ds' dh_clean @@ -1088,11 +1124,12 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.1+ds' dh_auto_build -- all testing/run_ataqv_tests - make -j3 "INSTALL=install --strip-program=true" all testing/run_ataqv_tests + make -j4 "INSTALL=install --strip-program=true" all testing/run_ataqv_tests make[2]: Entering directory '/build/reproducible-path/ataqv-1.3.1+ds' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/ataqv.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/ataqv.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/Features.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/HTS.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/IO.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/IO.cpp In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.hpp:12, @@ -1120,7 +1157,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/IO.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/IO.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/Metrics.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/Peaks.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, @@ -1175,7 +1211,6 @@ /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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/Utils.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.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 ‘std::vector PeakTree::list_peaks()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:200:14: @@ -1234,14 +1269,7 @@ 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/14/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -In file included from /usr/include/c++/14/map:62, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.hpp:12, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:18: -/usr/include/c++/14/bits/stl_tree.h: In function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: -/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/Utils.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.cpp /usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, @@ -1277,6 +1305,7 @@ /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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/run_ataqv_tests.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/run_ataqv_tests.cpp 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 Peak&, const Peak&)]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, inlined from ‘std::vector PeakTree::list_peaks_by_overlapping_hqaa_descending()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:212:14: @@ -1297,13 +1326,18 @@ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/run_ataqv_tests.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/run_ataqv_tests.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_features.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_hts.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:1: /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____167()’: /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:171:47: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] 171 | REQUIRE_THROWS_AS(collection.add(f), std::out_of_range); | ^~~~~~~~~~~~ +In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp:3: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____169()’: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp:200:57: warning: catching polymorphic type ‘class HTSException’ by value [-Wcatch-value=] + 200 | REQUIRE_THROWS_AS(record_to_string(header, record), HTSException); + | ^~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:76: @@ -1316,6 +1350,45 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +In file included from /usr/include/c++/14/map:62, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.hpp:12, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:18: +/usr/include/c++/14/bits/stl_tree.h: In function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: +/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_io.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_io.cpp +/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1876 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, + inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, + inlined from ‘void ____C_A_T_C_H____T_E_S_T____61()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:67:14: +/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 ‘void ____C_A_T_C_H____T_E_S_T____61()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:67:14: +/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 1822 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_metrics.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_peaks.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.hpp:16, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:21: /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp: In function ‘nlohmann::basic_json::basic_json(std::initializer_list >, bool, value_t) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’: @@ -1324,6 +1397,11 @@ | ^~~~~~~~~~ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp: In function ‘nlohmann::basic_json::basic_json(std::initializer_list >, bool, value_t) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’: /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp:2082:5: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 +In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:1: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____172()’: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:181:44: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] + 181 | REQUIRE_THROWS_AS(rpc.add(peak3), std::out_of_range); + | ^~~~~~~~~~~~ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp: In member function ‘nlohmann::json Library::to_json()’: /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1380:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 1380 | } @@ -1364,35 +1442,56 @@ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1378:5: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 1378 | }; | ^ -/usr/include/c++/14/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1876 | __introsort_loop(_RandomAccessIterator __first, +In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:3: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____170()’: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:173:56: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] + 173 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); + | ^~~~~~~~~~~~~ +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:178:56: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] + 178 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); + | ^~~~~~~~~~~~~ +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____243()’: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:249:52: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] + 249 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); + | ^~~~~~~~~~~~~ +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____252()’: +/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:259:52: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] + 259 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/14/memory:69, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:568: +/usr/include/c++/14/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’: +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -/usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, - inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, - inlined from ‘void ____C_A_T_C_H____T_E_S_T____61()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:67:14: -/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 ‘void ____C_A_T_C_H____T_E_S_T____61()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_features.cpp:67:14: -/usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 1822 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_hts.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp +/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, + inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, + inlined from ‘void ____C_A_T_C_H____T_E_S_T____155()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:166:68: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, + inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, + inlined from ‘void ____C_A_T_C_H____T_E_S_T____100()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:125:68: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, + inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, + inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, + inlined from ‘void ____C_A_T_C_H____T_E_S_T____100()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:131:70: +/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_pair.h:61, from /usr/include/c++/14/tuple:38, from /usr/include/c++/14/mutex:40, @@ -1474,6 +1573,12 @@ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 +In file included from /usr/include/c++/14/vector:72, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569: +/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 = nlohmann::basic_json<>; _Alloc = std::allocator >]’: +/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 + 700 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1570:1: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 @@ -1575,75 +1680,6 @@ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1568:5: note: parameter passing for argument of type ‘std::initializer_list >’ changed in GCC 7.1 1568 | }; | ^ -In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp:3: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____169()’: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_hts.cpp:200:57: warning: catching polymorphic type ‘class HTSException’ by value [-Wcatch-value=] - 200 | REQUIRE_THROWS_AS(record_to_string(header, record), HTSException); - | ^~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_io.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_io.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_metrics.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/test_peaks.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp -In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:1: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____172()’: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:181:44: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] - 181 | REQUIRE_THROWS_AS(rpc.add(peak3), std::out_of_range); - | ^~~~~~~~~~~~ -In file included from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:3: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____170()’: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:173:56: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] - 173 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); - | ^~~~~~~~~~~~~ -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:178:56: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] - 178 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); - | ^~~~~~~~~~~~~ -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____243()’: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:249:52: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] - 249 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); - | ^~~~~~~~~~~~~ -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____252()’: -/build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_metrics.cpp:259:52: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] - 259 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/14/memory:69, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:568: -/usr/include/c++/14/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’: -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 -In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, - inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, - inlined from ‘void ____C_A_T_C_H____T_E_S_T____155()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:166:68: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, - inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, - inlined from ‘void ____C_A_T_C_H____T_E_S_T____100()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:125:68: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; bool _TrivialValueTypes = false]’, - inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*]’ at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = Peak*; _Tp = Peak]’ at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Peak; _Alloc = std::allocator]’ at /usr/include/c++/14/bits/stl_vector.h:606:31, - inlined from ‘ReferencePeakCollection::ReferencePeakCollection(const ReferencePeakCollection&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.hpp:29:7, - inlined from ‘void ____C_A_T_C_H____T_E_S_T____100()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_peaks.cpp:131:70: -/usr/include/c++/14/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/vector:72, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569: -/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 = nlohmann::basic_json<>; _Alloc = std::allocator >]’: -/usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 - 700 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, size_type, const value_type&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’, inlined from ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator[](size_type) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp:3730:38: @@ -1683,6 +1719,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/IO.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/IO.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/Metrics.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/Peaks.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/Utils.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.cpp In file included from /usr/include/c++/14/bits/stl_algo.h:61, from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:7: @@ -1699,6 +1736,7 @@ 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/ataqv build/ataqv.o build/Features.o build/HTS.o build/IO.o build/Metrics.o build/Peaks.o build/Utils.o -Wl,-z,relro -Wl,-z,now -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono -lhts -lz -lncurses -lpthread In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.hpp:12, @@ -1808,7 +1846,6 @@ /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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o testing/Utils.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.cpp 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 Peak&, const Peak&)]’ at /usr/include/c++/14/bits/stl_algo.h:4805:18, inlined from ‘std::vector PeakTree::list_peaks_by_size_descending()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:224:14: @@ -1849,7 +1886,6 @@ /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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.1+ds/src/cpp -D LINUX -o build/ataqv build/ataqv.o build/Features.o build/HTS.o build/IO.o build/Metrics.o build/Peaks.o build/Utils.o -Wl,-z,relro -Wl,-z,now -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono -lhts -lz -lncurses -lpthread In file included from /usr/include/c++/14/map:62, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.hpp:12, @@ -2092,7 +2128,7 @@ make[2]: Leaving directory '/build/reproducible-path/ataqv-1.3.1+ds' make[1]: Leaving directory '/build/reproducible-path/ataqv-1.3.1+ds' dh_auto_test - make -j3 test + make -j4 test make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.1+ds' [E::sam_format1_append] Corrupted aux data for read SRR891268.122333488 flag 83 Reading human autosomal references from autosomal_references.gz. @@ -2149,7 +2185,7 @@ chr20 feature count: 694 chr21 feature count: 321 chr22 feature count: 593 -Loaded 24989 TSS in 3.89919 seconds. (6408.76 TSS/second). +Loaded 24989 TSS in 3.12566 seconds. (7994.78 TSS/second). Collecting metrics from test.bam. @@ -2332,7 +2368,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 38.6364 seconds. (964.789 peaks/second). +Loaded 37276 peaks in 31.2793 seconds. (1191.72 peaks/second). Logging problematic reads to SRR891278.problems. @@ -2513,7 +2549,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 38.421 seconds. (970.198 peaks/second). +Loaded 37276 peaks in 31.0769 seconds. (1199.48 peaks/second). New maximum proper pair fragment length: 42 from [SRR891275.608 1123 chr1 569907 57 42M = 569907 42 CACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAA @@@FFFEFFDHFBHIJIEFHJIGGF:CFGEDF?FFHEG@FGG XA:Z:chrM,+9359,42M,1; MD:Z:42 NM:i:0 AS:i:42 XS:i:37 RG:Z:SRR891275 PG:Z:MarkDuplicates] New maximum proper pair fragment length: 330 from [SRR891278.50 1123 chr1 569913 27 50M = 570193 330 NCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGC #1=DDFFFHHGHHJJJJIJJJGEGHIGGIIIJJJJIIFGGIJHIIJICHH XA:Z:chrM,+9365,50M,2; MD:Z:0C49 NM:i:1 AS:i:49 XS:i:44 RG:Z:SRR891278 PG:Z:MarkDuplicates-4FB7F45F] @@ -2551,12 +2587,12 @@ Added TSS coverage for chr2; thread count=1 Added TSS coverage for chr1; thread count=1 All TSS jobs started. Waiting for last ones to complete. -Calculated TSS coverage in 0.347089 seconds. +Calculated TSS coverage in 0.219645 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.000811763 seconds. +Calculated TSS metrics in 0.0005613 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.00185899 seconds. -Analyzed 1040 reads in 0.567816 seconds (1831.58 reads/second). +Calculated TSS metrics in 0.000505942 seconds. +Analyzed 1040 reads in 0.338814 seconds (3069.53 reads/second). ataqv 1.3.1 @@ -2966,7 +3002,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 39.159 seconds. (951.921 peaks/second). +Loaded 37276 peaks in 30.804 seconds. (1210.096 peaks/second). New maximum proper pair fragment length: 42 from [SRR891275.608 1123 chr1 569907 57 42M = 569907 42 CACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAA @@@FFFEFFDHFBHIJIEFHJIGGF:CFGEDF?FFHEG@FGG XA:Z:chrM,+9359,42M,1; MD:Z:42 NM:i:0 AS:i:42 XS:i:37 RG:Z:SRR891275 PG:Z:MarkDuplicates] New maximum proper pair fragment length: 330 from [SRR891278.50 1123 chr1 569913 27 50M = 570193 330 NCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGC #1=DDFFFHHGHHJJJJIJJJGEGHIGGIIIJJJJIIFGGIJHIIJICHH XA:Z:chrM,+9365,50M,2; MD:Z:0C49 NM:i:1 AS:i:49 XS:i:44 RG:Z:SRR891278 PG:Z:MarkDuplicates-4FB7F45F] @@ -2975,7 +3011,7 @@ New maximum proper pair fragment length: 609 from [SRR891275.714 99 chr1 79875808 60 50M = 79876367 609 GGCCCAGCCAAGTTGACACATAAAATAAACTTTCACAATATTGCAGGCAG @@@DDDFFFHAH build/$(basename $f); install -m 0755 build/$(basename $f) /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/bin; done +install -m 0755 build/ataqv /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/bin cp -a src/web/* /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/share/ataqv/web find /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/share/ataqv/web -type d -exec chmod 755 {} \; find /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/share/ataqv/web -type f -exec chmod 644 {} \; @@ -3157,14 +3193,14 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: debian/ataqv/usr/bin/ataqv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/ataqv/usr/lib/ataqv/run_ataqv_tests contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/ataqv/usr/bin/ataqv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ataqv-dbgsym' in '../ataqv-dbgsym_1.3.1+ds-2_armhf.deb'. dpkg-deb: building package 'ataqv' in '../ataqv_1.3.1+ds-2_armhf.deb'. +dpkg-deb: building package 'ataqv-dbgsym' in '../ataqv-dbgsym_1.3.1+ds-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../ataqv_1.3.1+ds-2_armhf.buildinfo dpkg-genchanges --build=binary -O../ataqv_1.3.1+ds-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3172,12 +3208,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/14019/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14019/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/19526 and its subdirectories -I: Current time: Mon Jan 13 01:45:26 -12 2025 -I: pbuilder-time-stamp: 1736775926 +I: removing directory /srv/workspace/pbuilder/14019 and its subdirectories +I: Current time: Tue Jan 14 03:52:31 +14 2025 +I: pbuilder-time-stamp: 1736776351