Diff of the two buildlogs: -- --- b1/build.log 2024-04-19 21:16:09.914144072 +0000 +++ b2/build.log 2024-04-19 21:19:43.489001151 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 22 15:35:50 -12 2025 -I: pbuilder-time-stamp: 1747971350 +I: Current time: Fri May 23 17:39:17 +14 2025 +I: pbuilder-time-stamp: 1747971557 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/960366/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1372482/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +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 May 23 03:39 /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/1372482/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1372482/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + 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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='0a01c4b30c824c82b8873b27ab0b5126' - 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='960366' - PS1='# ' - PS2='> ' + INVOCATION_ID=d9716f4bb7144269a886d762b8d0b8b3 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=1372482 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.4IFCklMQ/pbuilderrc_BMfi --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.4IFCklMQ/b1 --logfile b1/build.log pbbam_2.4.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.4IFCklMQ/pbuilderrc_HDsk --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.4IFCklMQ/b2 --logfile b2/build.log pbbam_2.4.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 22 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/960366/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 20 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1372482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +261,7 @@ Get: 89 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-cram all 0.7-5 [17.6 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1 [617 kB] -Fetched 60.3 MB in 1s (114 MB/s) +Fetched 60.3 MB in 0s (159 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19930 files and directories currently installed.) @@ -534,8 +566,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri May 23 03:36:12 UTC 2025. -Universal Time is now: Fri May 23 03:36:12 UTC 2025. +Local time is now: Fri May 23 03:39:37 UTC 2025. +Universal Time is now: Fri May 23 03:39:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -616,7 +648,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pbbam-2.4.0+dfsg/ && 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 > ../pbbam_2.4.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/1372482/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1372482/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pbbam-2.4.0+dfsg/ && 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 > ../pbbam_2.4.0+dfsg-1_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.4.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -715,67 +751,59 @@ [5/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [6/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamReader.cpp.o -MF tests/pbbam_test.p/src_test_BamReader.cpp.o.d -o tests/pbbam_test.p/src_test_BamReader.cpp.o -c ../tests/src/test_BamReader.cpp [7/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o -MF tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o.d -o tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o -c ../tests/src/test_AlignmentPrinter.cpp -[8/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamFile.cpp.o -MF tests/pbbam_test.p/src_test_BamFile.cpp.o.d -o tests/pbbam_test.p/src_test_BamFile.cpp.o -c ../tests/src/test_BamFile.cpp -[9/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp +[8/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp +[9/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamFile.cpp.o -MF tests/pbbam_test.p/src_test_BamFile.cpp.o.d -o tests/pbbam_test.p/src_test_BamFile.cpp.o -c ../tests/src/test_BamFile.cpp [10/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp -[11/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp +[11/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp +[12/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/BamFile.cpp.o -MF src/libpbbam.so.2.4.0.p/BamFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamFile.cpp.o -c ../src/BamFile.cpp +[13/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp ../tests/src/test_BamRecordImplCore.cpp: In member function ‘virtual void BAM_BamRecordImplCore_can_be_move_constructed_Test::TestBody()’: ../tests/src/test_BamRecordImplCore.cpp:425:73: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 425 | BamRecordImpl bam(std::move(BamRecordImplCoreTests::CreateBamImpl())); | ^ ../tests/src/test_BamRecordImplCore.cpp:425:73: note: remove ‘std::move’ call -[12/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp -[13/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/BamFile.cpp.o -MF src/libpbbam.so.2.4.0.p/BamFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamFile.cpp.o -c ../src/BamFile.cpp -[14/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond 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../src/FastaReader.cpp +[48/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp +[49/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp +[50/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FofnReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp [51/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o -c ../src/FormatUtils.cpp -[52/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp -[53/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp -../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: -../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] - 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call -../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] - 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call -[54/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp +[52/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FileUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp +[53/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp +[54/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp +[55/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/13/map:62, from ../include/pbbam/ProgramInfo.h:6, from ../include/pbbam/BamHeader.h:6, @@ -926,35 +954,45 @@ ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ -[55/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/FofnReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp -[56/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o -c ../src/IFastqWriter.cpp +[56/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o -c ../src/IndexedFastqTextReader.cpp [57/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o -c ../src/IFastaWriter.cpp -[58/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o -c ../src/IndexedFastqReaderImpl.cpp -[59/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp -[60/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o -c ../src/IndexedFastqTextReader.cpp -[61/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/MD5.cpp.o -MF src/libpbbam.so.2.4.0.p/MD5.cpp.o.d -o src/libpbbam.so.2.4.0.p/MD5.cpp.o -c ../src/MD5.cpp +[58/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp +../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: +../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] + 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call +../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] + 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call +[59/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/MD5.cpp.o -MF src/libpbbam.so.2.4.0.p/MD5.cpp.o.d -o src/libpbbam.so.2.4.0.p/MD5.cpp.o -c ../src/MD5.cpp +[60/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o -c ../src/IndexedFastqReaderImpl.cpp +[61/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o -c ../tests/src/test_BamRecordImplVariableData.cpp [62/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o -c ../src/KSeqReader.cpp -[63/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o -c ../src/LibraryInfo.cpp -[64/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp -[65/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong 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src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o -c ../src/LibraryInfo.cpp +[65/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp [66/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp -[74/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.4.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.4.0.p/RecordType.cpp.o -c ../src/RecordType.cpp -[75/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o -c ../src/RunMetadata.cpp -[76/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp +[72/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp +[73/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow 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-fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFile.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp +[76/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, - from ../include/pbbam/PbiIndexedBamReader.h:6, - from ../src/PbiIndexedBamReader.cpp:3: + from ../include/pbbam/DataSet.h:6, + from ../include/pbbam/PbiFilter.h:6, + from ../include/pbbam/PbiFilterQuery.h:6, + from ../src/PbiFilterQuery.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, @@ -964,21 +1002,20 @@ inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, - inlined from ‘PacBio::BAM::PbiFilter& PacBio::BAM::PbiFilter::operator=(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:203:28, - inlined from ‘void PacBio::BAM::PbiIndexedBamReader::PbiIndexedBamReaderPrivate::Filter(PacBio::BAM::PbiFilter)’ at ../src/PbiIndexedBamReader.cpp:36:35: + inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, + inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::None]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[77/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp +[77/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp +[78/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/BamFile.h:6, - from ../include/pbbam/DataSet.h:6, - from ../include/pbbam/PbiFilter.h:6, - from ../include/pbbam/PbiFilterQuery.h:6, - from ../src/PbiFilterQuery.cpp:3: + from ../include/pbbam/PbiIndexedBamReader.h:6, + from ../src/PbiIndexedBamReader.cpp:3: In destructor ‘std::unique_ptr<_Tp, _Dp>::~unique_ptr() [with _Tp = PacBio::BAM::internal::FilterWrapper::WrapperInterface; _Dp = std::default_delete]’, inlined from ‘PacBio::BAM::internal::FilterWrapper::~FilterWrapper()’ at ../include/pbbam/internal/PbiFilter.inl:38:8, inlined from ‘constexpr void std::destroy_at(_Tp*) [with _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/stl_construct.h:88:18, @@ -988,19 +1025,18 @@ inlined from ‘constexpr void std::_Destroy(_ForwardIterator, _ForwardIterator, allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = PacBio::BAM::internal::FilterWrapper]’ at /usr/include/c++/13/bits/alloc_traits.h:948:20, inlined from ‘constexpr std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = PacBio::BAM::internal::FilterWrapper; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/vector.tcc:250:21, inlined from ‘std::unique_ptr PacBio::BAM::internal::PbiFilterPrivate::DeepCopy()’ at ../include/pbbam/internal/PbiFilter.inl:143:32, - inlined from ‘PacBio::BAM::PbiFilter::PbiFilter(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:199:55, - inlined from ‘PacBio::BAM::PbiFilterCompositeBamReader& PacBio::BAM::PbiFilterCompositeBamReader::Filter(const PacBio::BAM::PbiFilter&) [with OrderByType = PacBio::BAM::Compare::None]’ at ../include/pbbam/internal/CompositeBamReader.inl:147:17: + inlined from ‘PacBio::BAM::PbiFilter& PacBio::BAM::PbiFilter::operator=(const PacBio::BAM::PbiFilter&)’ at ../include/pbbam/internal/PbiFilter.inl:203:28, + inlined from ‘void PacBio::BAM::PbiIndexedBamReader::PbiIndexedBamReaderPrivate::Filter(PacBio::BAM::PbiFilter)’ at ../src/PbiIndexedBamReader.cpp:36:35: /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[78/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp -[79/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp -[80/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp -[81/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -MF src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.cpp +[79/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -MF src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.cpp +[80/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp +[81/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp [82/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TagCollection.cpp.o -MF src/libpbbam.so.2.4.0.p/TagCollection.cpp.o.d -o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o -c ../src/TagCollection.cpp [83/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp [84/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp -[85/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamReader.cpp.o -c ../src/SamReader.cpp +[85/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp [86/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp ../src/SamTagCodec.cpp: In static member function ‘static PacBio::BAM::TagCollection PacBio::BAM::SamTagCodec::Decode(const std::string&)’: ../src/SamTagCodec.cpp:79:63: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; const_reference = const char&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] @@ -1014,52 +1050,60 @@ /usr/include/c++/13/bits/basic_string.h:1236:7: note: declared here 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT | ^~~~~~~~ -[87/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp -[88/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp +[87/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamReader.cpp.o -c ../src/SamReader.cpp +[88/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Version.cpp.o -MF src/libpbbam.so.2.4.0.p/Version.cpp.o.d -o src/libpbbam.so.2.4.0.p/Version.cpp.o -c ../src/Version.cpp [89/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o -MF src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o.d -o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o -c ../src/TimeUtils.cpp [90/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp -[91/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -c ../src/TextFileWriter.cpp -[92/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o -MF src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp -[93/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Version.cpp.o -MF src/libpbbam.so.2.4.0.p/Version.cpp.o.d -o src/libpbbam.so.2.4.0.p/Version.cpp.o -c ../src/Version.cpp -[94/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -c ../src/VirtualRegion.cpp -[95/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp -[96/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp -[97/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -c ../src/TextFileReader.cpp -[98/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp +[91/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp +[95/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong 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-Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp -[101/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp +[100/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp +[101/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp +[102/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp ../src/ZmwChunkedFastaReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastaReader::ZmwChunkedFastaReaderPrivate::ZmwChunkedFastaReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastaReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastaReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastaReader.cpp:78:48: note: remove ‘std::move’ call -[102/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp -[103/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp -[104/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Validator.cpp.o -MF src/libpbbam.so.2.4.0.p/Validator.cpp.o.d -o src/libpbbam.so.2.4.0.p/Validator.cpp.o -c ../src/Validator.cpp -[105/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp -[106/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp -[107/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp -[108/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp +[103/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/Validator.cpp.o -MF src/libpbbam.so.2.4.0.p/Validator.cpp.o.d -o src/libpbbam.so.2.4.0.p/Validator.cpp.o -c ../src/Validator.cpp +[104/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp +[105/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp +[106/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp +[107/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp +[108/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp +[109/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp +[110/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp +[111/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -c ../src/vcf/VcfFile.cpp +[112/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp +[113/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp +[114/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp ../src/ZmwChunkedFastqReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastqReader::ZmwChunkedFastqReaderPrivate::ZmwChunkedFastqReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastqReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastqReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastqReader.cpp:78:48: note: remove ‘std::move’ call -[109/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp -[110/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp -[111/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp -[112/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -c ../src/vcf/VcfFile.cpp -[113/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp -[114/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp -[115/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp -[116/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -c ../src/csv/CsvWriter.cpp -[117/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -c ../tests/src/test_BamRecordClipping.cpp -[118/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp -[119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp -[120/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -c src/PbbamVersion.cpp -[121/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp -[122/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp +[115/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -c ../src/csv/CsvWriter.cpp +[116/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp +[117/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp +[118/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp +[119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp +[120/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp +[121/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -c ../tests/src/test_BamRecordClipping.cpp +[122/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -c src/PbbamVersion.cpp +[123/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp +../src/vcf/VcfVariant.cpp: In member function ‘PacBio::VCF::VcfVariant& PacBio::VCF::VcfVariant::RemoveInfoField(const std::string&)’: +../src/vcf/VcfVariant.cpp:250:35: warning: redundant move in initialization [-Wredundant-move] + 250 | AddInfoField(std::move(field)); + | ~~~~~~~~~^~~~~~~ +../src/vcf/VcfVariant.cpp:250:35: note: remove ‘std::move’ call +[124/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp +[125/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, @@ -1082,60 +1126,53 @@ /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[123/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp -[124/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp -[125/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp -../src/vcf/VcfVariant.cpp: In member function ‘PacBio::VCF::VcfVariant& PacBio::VCF::VcfVariant::RemoveInfoField(const std::string&)’: -../src/vcf/VcfVariant.cpp:250:35: warning: redundant move in initialization [-Wredundant-move] - 250 | AddInfoField(std::move(field)); - | ~~~~~~~~~^~~~~~~ -../src/vcf/VcfVariant.cpp:250:35: note: remove ‘std::move’ call [126/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp -[127/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp -[128/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -c ../src/csv/CsvReader.cpp -[129/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp +[127/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp +[128/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp +[129/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -c ../src/csv/CsvReader.cpp [130/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BgzipWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o -c ../tests/src/test_BgzipWriter.cpp [131/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp -[132/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BedWriter.cpp.o -MF tests/pbbam_test.p/src_test_BedWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BedWriter.cpp.o -c ../tests/src/test_BedWriter.cpp -[133/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BedReader.cpp.o -MF tests/pbbam_test.p/src_test_BedReader.cpp.o.d -o tests/pbbam_test.p/src_test_BedReader.cpp.o -c ../tests/src/test_BedReader.cpp -[134/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o -c ../tests/src/test_BgzipFastaWriter.cpp -[135/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 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src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.4.0.p/MD5.cpp.o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.4.0.p/RecordType.cpp.o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.4.0.p/SamReader.cpp.o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o src/libpbbam.so.2.4.0.p/Tag.cpp.o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o src/libpbbam.so.2.4.0.p/Validator.cpp.o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o src/libpbbam.so.2.4.0.p/Version.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.4.0 -Wl,-z,relro -Wl,-z,now -g -O2 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-D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_StringUtils.cpp.o -MF tests/pbbam_test.p/src_test_StringUtils.cpp.o.d -o tests/pbbam_test.p/src_test_StringUtils.cpp.o -c ../tests/src/test_StringUtils.cpp +[169/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 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-Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_RunMetadata.cpp.o -MF tests/pbbam_test.p/src_test_RunMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_RunMetadata.cpp.o -c ../tests/src/test_RunMetadata.cpp +[172/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_SamIO.cpp.o -MF tests/pbbam_test.p/src_test_SamIO.cpp.o.d -o tests/pbbam_test.p/src_test_SamIO.cpp.o -c ../tests/src/test_SamIO.cpp In file included from /usr/include/c++/13/ios:45, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, @@ -1180,18 +1217,17 @@ /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ -[172/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 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/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/tests Generating test data in /build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/tests @@ -1213,20 +1249,15 @@ - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. -[186/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast 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-DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp -[194/226] c++ -Itests/zero_byte_check/zero_byte_check.p -Itests/zero_byte_check -I../tests/zero_byte_check -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp -[195/226] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[196/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp -[197/226] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[198/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp -[199/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Tags.cpp.o -MF tests/pbbam_test.p/src_test_Tags.cpp.o.d -o tests/pbbam_test.p/src_test_Tags.cpp.o -c ../tests/src/test_Tags.cpp +[186/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o -c ../tests/src/test_PbiFilterQuery.cpp +[187/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfSort.cpp.o -MF tests/pbbam_test.p/src_test_VcfSort.cpp.o.d -o tests/pbbam_test.p/src_test_VcfSort.cpp.o -c ../tests/src/test_VcfSort.cpp +[188/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp +[189/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 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-I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Version.cpp.o -MF tests/pbbam_test.p/src_test_Version.cpp.o.d -o tests/pbbam_test.p/src_test_Version.cpp.o -c ../tests/src/test_Version.cpp +[192/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp +[193/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilter.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.cpp +[194/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Tags.cpp.o -MF tests/pbbam_test.p/src_test_Tags.cpp.o.d -o tests/pbbam_test.p/src_test_Tags.cpp.o -c ../tests/src/test_Tags.cpp In file included from ../tests/src/test_Tags.cpp:14: In function ‘testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int]’, inlined from ‘static testing::AssertionResult testing::internal::EqHelper::Compare(const char*, const char*, const T1&, const T2&) [with T1 = unsigned int; T2 = unsigned int; typename std::enable_if<((! std::is_integral<_Tp>::value) || (! std::is_pointer<_Dp>::value))>::type* = 0]’ at /usr/include/gtest/gtest.h:1398:64, @@ -1248,27 +1279,32 @@ ../tests/src/test_Tags.cpp:327:14: note: ‘v2’ was declared here 327 | uint16_t v2; | ^~ -[200/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp +[195/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp +[196/226] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[197/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp +[198/226] c++ -Itests/zero_byte_check/zero_byte_check.p -Itests/zero_byte_check -I../tests/zero_byte_check -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp +[199/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp +[200/226] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [201/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -c ../tools/pbindex/src/PbIndexSettings.cpp -[202/226] c++ -o tools/pbindex tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 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-D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp +[214/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [215/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp -[216/226] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[217/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp -[218/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp -[219/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp -[220/226] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[216/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp +[217/226] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[218/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp +[219/226] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[220/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [221/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/data/FrameEncoders.h:8, @@ -1291,9 +1327,9 @@ /usr/include/c++/13/bits/unique_ptr.h:403:19: warning: potential null pointer dereference [-Wnull-dereference] 403 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[222/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp -[223/226] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[224/226] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o tests/pbbam_test.p/src_test_Compare.cpp.o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o tests/pbbam_test.p/src_test_Csv.cpp.o tests/pbbam_test.p/src_test_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o tests/pbbam_test.p/src_test_RunMetadata.cpp.o tests/pbbam_test.p/src_test_SamIO.cpp.o tests/pbbam_test.p/src_test_SegmentReads.cpp.o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o tests/pbbam_test.p/src_test_StringUtils.cpp.o tests/pbbam_test.p/src_test_Tags.cpp.o tests/pbbam_test.p/src_test_TextFileReader.cpp.o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o tests/pbbam_test.p/src_test_TimeUtils.cpp.o tests/pbbam_test.p/src_test_Validator.cpp.o tests/pbbam_test.p/src_test_VcfFile.cpp.o tests/pbbam_test.p/src_test_VcfFormat.cpp.o tests/pbbam_test.p/src_test_VcfHeader.cpp.o tests/pbbam_test.p/src_test_VcfReader.cpp.o tests/pbbam_test.p/src_test_VcfSort.cpp.o tests/pbbam_test.p/src_test_VcfQuery.cpp.o tests/pbbam_test.p/src_test_VcfVariant.cpp.o tests/pbbam_test.p/src_test_VcfWriter.cpp.o tests/pbbam_test.p/src_test_Version.cpp.o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[222/226] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o tests/pbbam_test.p/src_test_Compare.cpp.o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o tests/pbbam_test.p/src_test_Csv.cpp.o tests/pbbam_test.p/src_test_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o tests/pbbam_test.p/src_test_RunMetadata.cpp.o tests/pbbam_test.p/src_test_SamIO.cpp.o tests/pbbam_test.p/src_test_SegmentReads.cpp.o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o tests/pbbam_test.p/src_test_StringUtils.cpp.o tests/pbbam_test.p/src_test_Tags.cpp.o tests/pbbam_test.p/src_test_TextFileReader.cpp.o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o tests/pbbam_test.p/src_test_TimeUtils.cpp.o tests/pbbam_test.p/src_test_Validator.cpp.o tests/pbbam_test.p/src_test_VcfFile.cpp.o tests/pbbam_test.p/src_test_VcfFormat.cpp.o tests/pbbam_test.p/src_test_VcfHeader.cpp.o tests/pbbam_test.p/src_test_VcfReader.cpp.o tests/pbbam_test.p/src_test_VcfSort.cpp.o tests/pbbam_test.p/src_test_VcfQuery.cpp.o tests/pbbam_test.p/src_test_VcfVariant.cpp.o tests/pbbam_test.p/src_test_VcfWriter.cpp.o tests/pbbam_test.p/src_test_Version.cpp.o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[223/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp +[224/226] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [225/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp In file included from /usr/include/c++/13/memory:78, from /usr/include/pbcopper/logging/LogMessage.h:8, @@ -1451,7 +1487,7 @@ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ -PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ +PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" LD_LIBRARY_PATH="$LIBDIR:" \ cram3 -v --preserve-env tests/src/cram/pbbamify.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbbamify.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed @@ -1725,12 +1761,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1372482/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1372482/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/960366 and its subdirectories -I: Current time: Thu May 22 15:39:08 -12 2025 -I: pbuilder-time-stamp: 1747971548 +I: removing directory /srv/workspace/pbuilder/1372482 and its subdirectories +I: Current time: Fri May 23 17:42:42 +14 2025 +I: pbuilder-time-stamp: 1747971762