Diff of the two buildlogs: -- --- b1/build.log 2024-05-04 02:00:55.866360618 +0000 +++ b2/build.log 2024-05-04 02:04:13.005964168 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 3 13:46:59 -12 2024 -I: pbuilder-time-stamp: 1714787219 +I: Current time: Fri Jun 6 22:23:59 +14 2025 +I: pbuilder-time-stamp: 1749198239 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/1809995/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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 Jun 6 08:24 /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/2449465/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2449465/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a40613241e024ec9893dae5a2d36bae4' - 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='1809995' - PS1='# ' - PS2='> ' + INVOCATION_ID=ae596f662fa54648a96cbcbcd067fe7f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=2449465 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.L00M3GwF/pbuilderrc_DD31 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.L00M3GwF/b1 --logfile b1/build.log pbbam_2.4.0+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.L00M3GwF/pbuilderrc_1S2G --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.L00M3GwF/b2 --logfile b2/build.log pbbam_2.4.0+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 3 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1809995/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 5 14:06 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2449465/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -235,7 +267,7 @@ Get: 95 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-cram all 0.7-5 [17.6 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] -Fetched 64.3 MB in 4s (15.3 MB/s) +Fetched 64.3 MB in 1s (53.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19695 files and directories currently installed.) @@ -567,8 +599,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat May 4 01:50:28 UTC 2024. -Universal Time is now: Sat May 4 01:50:28 UTC 2024. +Local time is now: Fri Jun 6 08:25:12 UTC 2025. +Universal Time is now: Fri Jun 6 08:25:12 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -650,7 +682,11 @@ 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/2449465/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2449465/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 @@ -741,86 +777,146 @@ Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j20 -v -[1/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' -[2/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j42 -v +[1/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' +[2/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /build/reproducible-path/pbbam-2.4.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/226] 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 -fcf-protection -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_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/226] 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 -fcf-protection -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 -[5/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 -[7/226] 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 -fcf-protection -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 -[8/226] 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 -fcf-protection -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/BaiIndexCache.cpp.o -MF src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.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 -fcf-protection -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 -[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 -fcf-protection -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_BgzipFastqWriter.cpp.o -MF tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o -c ../tests/src/test_BgzipFastqWriter.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 -fcf-protection -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_CollectionMetadata.cpp.o -MF tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o -c ../tests/src/test_CollectionMetadata.cpp -[12/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 -[14/226] 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 -fcf-protection -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 -[15/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict 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-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/FaiZmwChunker.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp +[47/226] 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 -fcf-protection -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/BamRecordImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o -c ../src/BamRecordImpl.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 -fcf-protection -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/BgzipFastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o -c ../src/BgzipFastaWriter.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 -fcf-protection -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/FaiIndex.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.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 -fcf-protection -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/BamRecordTags.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.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 -fcf-protection -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/FileProducer.cpp.o -MF src/libpbbam.so.2.4.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o -c ../src/FileProducer.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 -fcf-protection -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/DataSetXsd.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.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 -fcf-protection -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/BgzipFastqWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.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 -fcf-protection -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/BamFileMerger.cpp.o -MF src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.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 -fcf-protection -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/FastaSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp +[56/226] 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 -fcf-protection -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 -[20/226] 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 -fcf-protection -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/BamTagCodec.cpp.o -MF src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp -[21/226] 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 -fcf-protection -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/BamRecordView.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o -c ../src/BamRecordView.cpp -[22/226] 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 -fcf-protection -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/BgzipWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o -c ../src/BgzipWriter.cpp -[23/226] 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 -fcf-protection -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_CompositeBamReaders.cpp.o -MF tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o.d -o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o -c ../tests/src/test_CompositeBamReaders.cpp -[24/226] 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 -fcf-protection -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 -[25/226] 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 -fcf-protection -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/BamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/BamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamReader.cpp.o -c ../src/BamReader.cpp -[26/226] 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 -fcf-protection -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/Config.cpp.o -MF src/libpbbam.so.2.4.0.p/Config.cpp.o.d -o src/libpbbam.so.2.4.0.p/Config.cpp.o -c ../src/Config.cpp -[27/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/DataSet.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSet.cpp.o -c ../src/DataSet.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 -fcf-protection -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 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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 -fcf-protection -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 +[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 -fcf-protection -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] + 79 | tags[name] = Tag{static_cast(remainder[0], TagModifier::ASCII_CHAR)}; + | ^ +In file included from /usr/include/c++/13/string:54, + from ../include/pbbam/Tag.h:7, + from ../include/pbbam/TagCollection.h:6, + from ../include/pbbam/SamTagCodec.h:6, + from ../src/SamTagCodec.cpp:3: +/usr/include/c++/13/bits/basic_string.h:1236:7: note: declared here + 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT + | ^~~~~~~~ +[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 -fcf-protection -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 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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 +[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 -fcf-protection -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, @@ -971,140 +1067,105 @@ ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ -[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 -fcf-protection -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/IndexedBamWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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/IndexedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.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 -fcf-protection -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 -[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 -fcf-protection -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/IndexedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o -c ../src/IndexedFastqReader.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 -fcf-protection -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/PbiBuilder.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[86/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 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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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 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-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 -[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 -fcf-protection -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 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-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 -fcf-protection -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 -[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 -fcf-protection -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] - 79 | tags[name] = Tag{static_cast(remainder[0], TagModifier::ASCII_CHAR)}; - | ^ -In file included from /usr/include/c++/13/string:54, - from ../include/pbbam/Tag.h:7, - from ../include/pbbam/TagCollection.h:6, - from ../include/pbbam/SamTagCodec.h:6, - from ../src/SamTagCodec.cpp:3: -/usr/include/c++/13/bits/basic_string.h:1236:7: note: declared here - 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT - | ^~~~~~~~ -[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 -fcf-protection -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 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-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 -[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 -fcf-protection -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 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-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 -fcf-protection -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 -fcf-protection -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 -[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[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 -fcf-protection -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 +[130/226] 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 -fcf-protection -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 -[118/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 +[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 -fcf-protection -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/BamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp +[132/226] 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 -fcf-protection -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 +[133/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[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 -fcf-protection -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 -[130/226] 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 -fcf-protection -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 -[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 -fcf-protection -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 +[134/226] 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 -fcf-protection -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 -[132/226] 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 -fcf-protection -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 -[133/226] 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 -fcf-protection -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 -[134/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond 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-O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[138/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond 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src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp -[140/226] 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 -fcf-protection -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_FastaCache.cpp.o -MF tests/pbbam_test.p/src_test_FastaCache.cpp.o.d -o tests/pbbam_test.p/src_test_FastaCache.cpp.o -c ../tests/src/test_FastaCache.cpp -[141/226] 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 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src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o 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,-soname,libpbbam.so.2.4.0 -Wl,-z,relro 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-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 +[142/226] 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 -fcf-protection -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 +[143/226] 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 -fcf-protection -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 +[144/226] 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 -fcf-protection -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 +[145/226] 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 -fcf-protection -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 +[146/226] 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 -fcf-protection -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 +[147/226] 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 -fcf-protection -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_Pulse2BaseCache.cpp.o -MF tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o.d -o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o -c ../tests/src/test_Pulse2BaseCache.cpp +[148/226] 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 -fcf-protection -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 +[149/226] 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 -fcf-protection -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 +[150/226] 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 -fcf-protection -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/Tag.cpp.o -MF src/libpbbam.so.2.4.0.p/Tag.cpp.o.d -o src/libpbbam.so.2.4.0.p/Tag.cpp.o -c ../src/Tag.cpp +[151/226] 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 -fcf-protection -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 +[152/226] 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 -fcf-protection -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_SequenceUtils.cpp.o -MF tests/pbbam_test.p/src_test_SequenceUtils.cpp.o.d -o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o -c ../tests/src/test_SequenceUtils.cpp +[153/226] /usr/bin/python3 ../tests/scripts/generate_data.py /build/reproducible-path/pbbam-2.4.0+dfsg/tests/data /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/tests +Generating test data in /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/tests + - Creating file: truncated.bam...done. + - Creating file: chunking_emptyfilters.subreadset.xml...done. + - Creating file: chunking_missingfilters.subreadset.xml...done. + - Creating file: normal.fa...done. + - Creating file: normal.fq...done. + - Creating symlink: aligned.bam...done. + - Creating symlink: aligned.bam.bai...done. + - Creating symlink: aligned.bam.pbi...done. + - Creating symlink: aligned2.bam...done. + - Creating symlink: aligned2.bam.bai...done. + - Creating symlink: aligned2.bam.pbi...done. + - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. + - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. + - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. + - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. + - 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. +[154/226] 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 -fcf-protection -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 +[155/226] 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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-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 +[157/226] 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 -fcf-protection -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 +[158/226] 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 -fcf-protection -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 +[159/226] 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 -fcf-protection -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_TimeUtils.cpp.o -MF tests/pbbam_test.p/src_test_TimeUtils.cpp.o.d -o tests/pbbam_test.p/src_test_TimeUtils.cpp.o -c ../tests/src/test_TimeUtils.cpp +[160/226] 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 -fcf-protection -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_VcfFile.cpp.o -MF tests/pbbam_test.p/src_test_VcfFile.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFile.cpp.o -c ../tests/src/test_VcfFile.cpp +[161/226] 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 -fcf-protection -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 +[162/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include 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-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 -fcf-protection -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 +[184/226] 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 -fcf-protection -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_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -c ../tools/pbindexdump/src/CppFormatter.cpp +[185/226] 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 -fcf-protection -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 +[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 -fcf-protection -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_VcfHeader.cpp.o -MF tests/pbbam_test.p/src_test_VcfHeader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfHeader.cpp.o -c ../tests/src/test_VcfHeader.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 -fcf-protection -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, @@ -1149,72 +1210,49 @@ /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ -[173/226] 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 -fcf-protection -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 -[174/226] 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 -fcf-protection -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_TextFileWriter.cpp.o -MF tests/pbbam_test.p/src_test_TextFileWriter.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o -c ../tests/src/test_TextFileWriter.cpp -[175/226] 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 -fcf-protection -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_PacBioIndex.cpp.o -MF tests/pbbam_test.p/src_test_PacBioIndex.cpp.o.d -o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o -c ../tests/src/test_PacBioIndex.cpp -[176/226] 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 -fcf-protection -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_TextFileReader.cpp.o -MF tests/pbbam_test.p/src_test_TextFileReader.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileReader.cpp.o -c ../tests/src/test_TextFileReader.cpp -[177/226] /usr/bin/python3 ../tests/scripts/generate_data.py /build/reproducible-path/pbbam-2.4.0+dfsg/tests/data /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/tests -Generating test data in /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/tests - - Creating file: truncated.bam...done. - - Creating file: chunking_emptyfilters.subreadset.xml...done. - - Creating file: chunking_missingfilters.subreadset.xml...done. - - Creating file: normal.fa...done. - - Creating file: normal.fq...done. - - Creating symlink: aligned.bam...done. - - Creating symlink: aligned.bam.bai...done. - - Creating symlink: aligned.bam.pbi...done. - - Creating symlink: aligned2.bam...done. - - Creating symlink: aligned2.bam.bai...done. - - Creating symlink: aligned2.bam.pbi...done. - - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - - 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. -[178/226] 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 -fcf-protection -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_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.cpp -[179/226] 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 -fcf-protection -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_VcfHeader.cpp.o -MF tests/pbbam_test.p/src_test_VcfHeader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfHeader.cpp.o -c ../tests/src/test_VcfHeader.cpp -[180/226] 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 -fcf-protection -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_ReadGroupHashing.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -c ../tests/src/test_ReadGroupHashing.cpp -[181/226] 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 -fcf-protection -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 -[182/226] 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 -fcf-protection -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_VcfFormat.cpp.o -MF tests/pbbam_test.p/src_test_VcfFormat.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFormat.cpp.o -c ../tests/src/test_VcfFormat.cpp -[183/226] 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 -fcf-protection -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 -[184/226] 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 -fcf-protection -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_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp -[185/226] 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 -fcf-protection -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_VcfVariant.cpp.o -MF tests/pbbam_test.p/src_test_VcfVariant.cpp.o.d -o tests/pbbam_test.p/src_test_VcfVariant.cpp.o -c ../tests/src/test_VcfVariant.cpp -[186/226] 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 -fcf-protection -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 -[187/226] 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 -fcf-protection -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 -[188/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/x86_64-linux-gnu/libhts.so -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group -[189/226] 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 -fcf-protection -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 -[190/226] 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 -fcf-protection -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 -[191/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 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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 -[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 -fcf-protection -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 -[217/226] 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 -fcf-protection -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 -[218/226] 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 -fcf-protection -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 -[219/226] 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 -fcf-protection -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 +[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 -fcf-protection -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 +[189/226] c++ -o src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/BamFile.cpp.o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.4.0.p/BamHeader.cpp.o src/libpbbam.so.2.4.0.p/BamReader.cpp.o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/BamWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.4.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.4.0.p/Compare.cpp.o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.4.0.p/Config.cpp.o src/libpbbam.so.2.4.0.p/DataSet.cpp.o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o 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,-soname,libpbbam.so.2.4.0 -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,--start-group /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[190/226] /usr/bin/meson --internal symbolextractor /build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/libpbbam.so.2.4.0.symbols +[191/226] 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 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[192/226] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[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 -fcf-protection -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_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.cpp +[194/226] 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 -fcf-protection -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_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp +[195/226] 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 -fcf-protection -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_VcfVariant.cpp.o -MF tests/pbbam_test.p/src_test_VcfVariant.cpp.o.d -o tests/pbbam_test.p/src_test_VcfVariant.cpp.o -c ../tests/src/test_VcfVariant.cpp +[196/226] 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 -fcf-protection -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_main.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/main.cpp +[197/226] 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 -fcf-protection -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_VcfFormat.cpp.o -MF tests/pbbam_test.p/src_test_VcfFormat.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFormat.cpp.o -c ../tests/src/test_VcfFormat.cpp +[198/226] 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 -fcf-protection -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 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-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 -fcf-protection -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_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 +[201/226] 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 -fcf-protection -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_ZmwChunkedFastxReader.cpp.o -MF tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -c ../tests/src/test_ZmwChunkedFastxReader.cpp +[202/226] 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 -fcf-protection -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_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp +[203/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 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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 +[205/226] 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 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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/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 +[207/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[208/226] 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 -fcf-protection -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_ZmwQuery.cpp.o -MF tests/pbbam_test.p/src_test_ZmwQuery.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -c ../tests/src/test_ZmwQuery.cpp +[209/226] 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 -fcf-protection -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_Validator.cpp.o -MF tests/pbbam_test.p/src_test_Validator.cpp.o.d -o tests/pbbam_test.p/src_test_Validator.cpp.o -c ../tests/src/test_Validator.cpp +[210/226] 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 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tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp +[212/226] 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 -fcf-protection -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 +[213/226] 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 -fcf-protection -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 +[214/226] 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 -fcf-protection -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 +[215/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[216/226] 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 -fcf-protection -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_SegmentReads.cpp.o -MF tests/pbbam_test.p/src_test_SegmentReads.cpp.o.d -o tests/pbbam_test.p/src_test_SegmentReads.cpp.o -c ../tests/src/test_SegmentReads.cpp +[217/226] 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 -fcf-protection -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 +[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 -fcf-protection -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 +[219/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[220/226] 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 -fcf-protection -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 +[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 -fcf-protection -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, @@ -1236,13 +1274,11 @@ ../tests/src/test_Tags.cpp:327:14: note: ‘v2’ was declared here 327 | uint16_t v2; | ^~ -[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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group -[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 -fcf-protection -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 -[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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-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 -fcf-protection -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 -[226/226] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[222/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp +[223/226] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/pbbam-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group +[224/226] 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 -fcf-protection -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 +[225/226] 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 -fcf-protection -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 +[226/226] 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/reproducible-path/pbbam-2.4.0+dfsg/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/pbbam-2.4.0+dfsg' sed \ @@ -1376,7 +1412,7 @@ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${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 @@ -1463,8 +1499,8 @@ Found ninja-1.11.1 at /usr/bin/ninja [1/15] Generating tests/pbbam_generate_data with a custom command -[2/15] Generating src/LibraryGitHash.h with a custom command -[3/14] Generating src/PbbamGitHash.cpp with a custom command +[2/15] Generating src/PbbamGitHash.cpp with a custom command +[3/14] Generating src/LibraryGitHash.h with a custom command [3/4] Installing files. Installing src/libpbbam.so.2.4.0 to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /build/reproducible-path/pbbam-2.4.0+dfsg/debian/tmp/usr/bin @@ -1639,11 +1675,11 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in '../libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_amd64.deb'. -dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-1_amd64.deb'. +dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.4.0+dfsg-1_amd64.deb'. dpkg-deb: building package 'libpbbam2.4.0' in '../libpbbam2.4.0_2.4.0+dfsg-1_amd64.deb'. -dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.4.0+dfsg-1_amd64.deb'. +dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in '../libpbbam2.4.0-dbgsym_2.4.0+dfsg-1_amd64.deb'. +dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.4.0+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.4.0+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1651,12 +1687,14 @@ 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/2449465/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2449465/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/1809995 and its subdirectories -I: Current time: Fri May 3 14:00:54 -12 2024 -I: pbuilder-time-stamp: 1714788054 +I: removing directory /srv/workspace/pbuilder/2449465 and its subdirectories +I: Current time: Fri Jun 6 22:27:12 +14 2025 +I: pbuilder-time-stamp: 1749198432