Diff of the two buildlogs: -- --- b1/build.log 2024-04-17 06:41:30.541305443 +0000 +++ b2/build.log 2024-04-17 06:50:10.247189255 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 16 18:35:34 -12 2024 -I: pbuilder-time-stamp: 1713335734 +I: Current time: Wed Apr 17 20:41:39 +14 2024 +I: pbuilder-time-stamp: 1713336099 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying reproducible_build I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23139/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/5594/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 17 06:41 /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/5594/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/5594/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='3e17b36b055048239ccc8f481b4ad3c7' - 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='23139' - PS1='# ' - PS2='> ' + INVOCATION_ID=6e123b4225944ab3bd9ce6e5cfcb06b5 + 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=5594 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.9enAAZcF/pbuilderrc_hXrx --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.9enAAZcF/b1 --logfile b1/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+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.9enAAZcF/pbuilderrc_mlDK --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.9enAAZcF/b2 --logfile b2/build.log ataqv_1.3.1+ds-2.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32z 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 16 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/23139/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/5594/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -272,7 +304,7 @@ Get: 123 http://deb.debian.org/debian trixie/main armhf node-d3-zoom all 1.8.3+~1.8.4-1 [26.8 kB] Get: 124 http://deb.debian.org/debian trixie/main armhf node-d3 all 5.16.0+~cs5.28.10-2 [223 kB] Get: 125 http://deb.debian.org/debian trixie/main armhf node-normalize.css all 8.0.1-5 [12.7 kB] -Fetched 56.2 MB in 1s (51.3 MB/s) +Fetched 56.2 MB in 1s (39.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19635 files and directories currently installed.) @@ -690,8 +722,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Apr 17 06:36:33 UTC 2024. -Universal Time is now: Wed Apr 17 06:36:33 UTC 2024. +Local time is now: Wed Apr 17 06:42:51 UTC 2024. +Universal Time is now: Wed Apr 17 06:42:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:armhf (1.83.0-2+b2) ... @@ -795,7 +827,11 @@ 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/5594/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/5594/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 @@ -805,7 +841,7 @@ 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 @@ -836,11 +872,12 @@ 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 -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 -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 -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 -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++/13/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, @@ -891,7 +928,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 -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 -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++/13/bits/stl_algo.h:61, @@ -926,6 +962,7 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, ReferencePeakCollection>, std::_Select1st, ReferencePeakCollection> >, numeric_string_comparator, std::allocator, ReferencePeakCollection> > >::const_iterator’ changed in GCC 7.1 2458 | _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 -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 file included from /usr/include/c++/13/map:63: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = ReferencePeakCollection; _Compare = numeric_string_comparator; _Alloc = std::allocator, ReferencePeakCollection> >]’, inlined from ‘ReferencePeakCollection* PeakTree::get_reference_peaks(const std::string&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:121:32: @@ -945,7 +982,6 @@ 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 -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 -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++/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_less_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, @@ -1014,18 +1050,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 /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 = Peak; _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, | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/13/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++/13/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++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -1096,39 +1125,13 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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 -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 -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.hpp:6, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:19: -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Feature&}; _Tp = Feature; _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 file included from /usr/include/c++/13/vector:66: -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Feature; _Alloc = std::allocator]’, - inlined from ‘void MetricsCollector::load_excluded_regions()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:700:39: -/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); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/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>:: - | ^~~~~~~~~~~~~~~~~~~ +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 -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); | ^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _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/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const nlohmann::basic_json, std::allocator >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’: -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’, - inlined from ‘void nlohmann::basic_json::push_back(const nlohmann::basic_json&) [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:5311:33: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ 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 /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:76: @@ -1136,16 +1139,24 @@ /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 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); + | ^~~~~~~~~~~~ /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_less_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, | ^~~~~~~~~~~~~~~~ /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 member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, - inlined from ‘void Metrics::add_alignment(const bam_hdr_t*, const bam1_t*)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:893:59: -/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 /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++/13/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++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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_less_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, @@ -1174,6 +1185,61 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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 -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 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Utils.hpp:6, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:19: +/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Feature&}; _Tp = Feature; _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 file included from /usr/include/c++/13/vector:66: +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Feature; _Alloc = std::allocator]’, + inlined from ‘void MetricsCollector::load_excluded_regions()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:700:39: +/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); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/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 long double&}; _Tp = long double; _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/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const nlohmann::basic_json, std::allocator >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’: +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’, + inlined from ‘void nlohmann::basic_json::push_back(const nlohmann::basic_json&) [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:5311:33: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 -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 +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]’, + inlined from ‘void Metrics::add_alignment(const bam_hdr_t*, const bam1_t*)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:893:59: +/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/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -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_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 /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/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]’: @@ -1247,7 +1313,19 @@ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp:277:15: note: ‘’ declared here 277 | j = BasicJsonType{}; | ~~^~~~~~~~~~~~~~~~~ -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 -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 /usr/include/c++/13/vector:72, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/run_ataqv_tests.cpp:2: +/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _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 file included from /usr/include/c++/13/vector:66: +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’, + inlined from ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:6057:43: +/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 ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = nlohmann::basic_json<>::json_value]’, inlined from ‘nlohmann::basic_json::value_type& nlohmann::basic_json::operator=(nlohmann::basic_json) [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:2554:13, inlined from ‘static void nlohmann::detail::external_constructor::construct(BasicJsonType&, typename BasicJsonType::number_float_t) [with BasicJsonType = nlohmann::basic_json<>]’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp:277:15, @@ -1424,6 +1502,12 @@ /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/json.hpp:277:15: note: ‘’ declared here 277 | j = BasicJsonType{}; | ~~^~~~~~~~~~~~~~~~~ +In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’, + inlined from ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:6057:43, + inlined from ‘Catch::Section::~Section()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:7923:53: +/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 = nlohmann::basic_json<>; _Alloc = std::allocator >]’, inlined from ‘nlohmann::json Metrics::to_json()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1462:28: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 @@ -1545,6 +1629,13 @@ 1570 | } | ^ /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++/13/memory:69, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:568: +/usr/include/c++/13/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++/13/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++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ 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 1570 | } | ^ @@ -1569,68 +1660,6 @@ /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 -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 -In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::basic_json, std::allocator >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’, - inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from ‘void nlohmann::basic_json::push_back(nlohmann::basic_json&&) [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:5275:33, - inlined from ‘nlohmann::json MetricsCollector::to_json()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1588:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/run_ataqv_tests.cpp:2: -/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _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 file included from /usr/include/c++/13/vector:66: -In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]’, - inlined from ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:6057:43: -/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 = Catch::SectionEndInfo; _Alloc = std::allocator]’, - inlined from ‘virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:6057:43, - inlined from ‘Catch::Section::~Section()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:7923:53: -/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/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -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 -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++/13/memory:69, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:568: -/usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_uninitialized.h:373:37, @@ -1640,6 +1669,18 @@ /usr/include/c++/13/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++/13/vector:72, + from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569: +/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/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: +/usr/include/c++/13/bits/stl_vector.h:1437:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 + 1437 | _M_fill_insert(begin() + __offset, __n, __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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++/13/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++/13/bits/stl_uninitialized.h:373:37, @@ -1658,19 +1699,14 @@ /usr/include/c++/13/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++/13/vector:72, - from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/catch.hpp:569: -/usr/include/c++/13/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++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type ‘std::vector, std::allocator > >::iterator’ changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/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: -/usr/include/c++/13/bits/stl_vector.h:1437:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 - 1437 | _M_fill_insert(begin() + __offset, __n, __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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_utils.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/test_utils.cpp +In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::basic_json, std::allocator >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’, + inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator >]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from ‘void nlohmann::basic_json::push_back(nlohmann::basic_json&&) [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:5275:33, + inlined from ‘nlohmann::json MetricsCollector::to_json()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Metrics.cpp:1588:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >’ changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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/Features.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Features.cpp In file included from /usr/include/c++/13/map:62, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.hpp:10, @@ -1703,7 +1739,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >*, std::vector > > >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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/HTS.o -c /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/HTS.cpp /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Feature&}; _Tp = Feature; _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>:: @@ -1723,9 +1758,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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/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 -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 -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 -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 -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++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:7: @@ -1768,6 +1805,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -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 /usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -1869,7 +1907,6 @@ /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/ataqv-1.3.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -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 member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Peak; _Alloc = std::allocator]’, inlined from ‘std::vector PeakTree::list_peaks_by_size_descending()’ at /build/reproducible-path/ataqv-1.3.1+ds/src/cpp/Peaks.cpp:221:28: /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 @@ -1920,7 +1957,6 @@ /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 -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++/13/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, @@ -2365,7 +2401,7 @@ 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 Reading human autosomal references from autosomal_references.gz. @@ -2422,7 +2458,7 @@ chr20 feature count: 694 chr21 feature count: 321 chr22 feature count: 593 -Loaded 24989 TSS in 3.14255 seconds. (7951.83 TSS/second). +Loaded 24989 TSS in 3.89639 seconds. (6413.37 TSS/second). Collecting metrics from test.bam. @@ -2605,7 +2641,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 31.2207 seconds. (1193.95 peaks/second). +Loaded 37276 peaks in 38.5697 seconds. (966.459 peaks/second). Logging problematic reads to SRR891278.problems. @@ -2786,7 +2822,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 30.873 seconds. (1207.4 peaks/second). +Loaded 37276 peaks in 38.6704 seconds. (963.94 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] @@ -2824,12 +2860,12 @@ 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 0.235908 seconds. +Calculated TSS coverage in 0.306939 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.0005325 seconds. +Calculated TSS metrics in 0.000843701 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.0005463 seconds. -Analyzed 1040 reads in 0.377998 seconds (2751.34 reads/second). +Calculated TSS metrics in 0.00084808 seconds. +Analyzed 1040 reads in 0.486677 seconds (2136.94 reads/second). ataqv 1.3.1 @@ -3239,7 +3275,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 30.874 seconds. (1207.357 peaks/second). +Loaded 37276 peaks in 40.274 seconds. (925.565 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] @@ -3248,7 +3284,7 @@ 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 -d -m 0755 /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/share/ataqv/web install -m 0755 build/ataqv /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/bin -for f in src/scripts/make_ataqv_pipeline src/scripts/mkarv src/scripts/run_ataqv_example src/scripts/srvarv; do sed -e 's/{{VERSION}}/1.3.1/g' $f > build/$(basename $f); install -m 0755 build/$(basename $f) /build/reproducible-path/ataqv-1.3.1+ds/debian/ataqv/usr/bin; done 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 {} \; @@ -3426,8 +3462,8 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -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 @@ -3441,12 +3477,14 @@ 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/5594/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/5594/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/23139 and its subdirectories -I: Current time: Tue Apr 16 18:41:07 -12 2024 -I: pbuilder-time-stamp: 1713336067 +I: removing directory /srv/workspace/pbuilder/5594 and its subdirectories +I: Current time: Wed Apr 17 20:49:17 +14 2024 +I: pbuilder-time-stamp: 1713336557