Diff of the two buildlogs: -- --- b1/build.log 2023-04-27 17:32:33.024843829 +0000 +++ b2/build.log 2023-04-27 17:14:56.235735618 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 27 05:15:01 -12 2023 -I: pbuilder-time-stamp: 1682615701 +I: Current time: Thu May 30 13:00:24 +14 2024 +I: pbuilder-time-stamp: 1717023624 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./pbbam_2.1.0+dfsg.orig.tar.xz] I: copying [./pbbam_2.1.0+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Oct 5 21:43:04 2022 -12 +gpgv: Signature made Thu Oct 6 23:43:04 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,52 +30,84 @@ dpkg-source: info: applying results_with_latest_samtools.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9386/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 30 13:00 /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/18953/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='9386' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=18953 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.HZ241JvN/pbuilderrc_bdIc --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HZ241JvN/b1 --logfile b1/build.log pbbam_2.1.0+dfsg-2.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.HZ241JvN/pbuilderrc_0QP3 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HZ241JvN/b2 --logfile b2/build.log --extrapackages usrmerge pbbam_2.1.0+dfsg-2.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink10-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 25 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9386/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 29 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +258,7 @@ Get: 87 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 python3-cram all 0.7-5 [17.6 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] -Fetched 55.7 MB in 1s (51.0 MB/s) +Fetched 55.7 MB in 5s (11.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -598,8 +630,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/pbbam-2.1.0+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_2.1.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/pbbam-2.1.0+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_2.1.0+dfsg-2_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.1.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -609,11 +650,11 @@ debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt binnengegaan dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-2.1.0+dfsg/gendata -make[1]: Leaving directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt verlaten dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary @@ -688,65 +729,51 @@ Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -v -[1/224] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' -[2/224] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' +[1/224] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' +[2/224] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.1.0 /build/pbbam-2.1.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp -[4/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.2.1.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.2.1.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp -[5/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.2.1.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.2.1.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp -[6/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[4/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[5/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[6/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.2.1.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.2.1.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [7/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[8/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[9/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp +[8/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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-Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/Compare.cpp.o -MF src/libpbbam.so.2.1.0.p/Compare.cpp.o.d -o src/libpbbam.so.2.1.0.p/Compare.cpp.o -c ../src/Compare.cpp -[28/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp -[29/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp -[30/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp -[31/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp -[32/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ErrnoReason.cpp.o -MF src/libpbbam.so.2.1.0.p/ErrnoReason.cpp.o.d -o src/libpbbam.so.2.1.0.p/ErrnoReason.cpp.o -c ../src/ErrnoReason.cpp -[33/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp -[34/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSet.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSet.cpp.o -c ../src/DataSet.cpp -[35/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[36/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp -[37/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FaiIndex.cpp.o -MF src/libpbbam.so.2.1.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.2.1.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.cpp -[38/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FaiZmwChunker.cpp.o -MF src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp -[39/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp -[40/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp -[41/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp -[42/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaCache.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp -[43/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp -[44/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FileProducer.cpp.o -MF src/libpbbam.so.2.1.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp -In file included from /usr/include/c++/12/string:40, - from ../src/FileProducer.h:6, - from ../src/FileProducer.cpp:3: -In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, - inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, - inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, - inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, - inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, - inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, - inlined from ‘PacBio::BAM::FileProducer::FileProducer(std::string, std::string)’ at ../src/FileProducer.cpp:29:25: -/usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] - 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[45/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp -[46/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp +[23/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/BgzipFastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/BgzipFastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.cpp +[24/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ChemistryTable.cpp.o -MF src/libpbbam.so.2.1.0.p/ChemistryTable.cpp.o.d -o src/libpbbam.so.2.1.0.p/ChemistryTable.cpp.o -c ../src/ChemistryTable.cpp +[25/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/Config.cpp.o -MF src/libpbbam.so.2.1.0.p/Config.cpp.o.d -o src/libpbbam.so.2.1.0.p/Config.cpp.o -c ../src/Config.cpp +[26/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp +[27/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/CollectionMetadata.cpp.o -MF src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o.d -o src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o -c ../src/CollectionMetadata.cpp +[28/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/BamRecord.cpp.o -MF src/libpbbam.so.2.1.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.2.1.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp +[29/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/Compare.cpp.o -MF src/libpbbam.so.2.1.0.p/Compare.cpp.o.d -o src/libpbbam.so.2.1.0.p/Compare.cpp.o -c ../src/Compare.cpp +[30/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp +[31/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp +[32/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp +[33/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference 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-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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp +[42/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp +[43/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaCache.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp +[44/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp +[45/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/12/map:60, from ../include/pbbam/ProgramInfo.h:6, from ../include/pbbam/BamHeader.h:6, @@ -897,10 +924,25 @@ ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ +[46/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FileProducer.cpp.o -MF src/libpbbam.so.2.1.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp +In file included from /usr/include/c++/12/string:40, + from ../src/FileProducer.h:6, + from ../src/FileProducer.cpp:3: +In static member function ‘static constexpr std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)’, + inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:423:21, + inlined from ‘static constexpr void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:418:7, + inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Allocator>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_replace(size_type, size_type, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.tcc:532:22, + inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::assign(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:1647:19, + inlined from ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/basic_string.h:815:28, + inlined from ‘PacBio::BAM::FileProducer::FileProducer(std::string, std::string)’ at ../src/FileProducer.cpp:29:25: +/usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] + 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ [47/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o -c ../src/FastaWriter.cpp -[48/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp -[49/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FofnReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp -[50/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FileUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp +[48/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp +[49/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp +[50/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FofnReader.cpp.o -MF src/libpbbam.so.2.1.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp +[51/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FileUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/boost/function/function_base.hpp:16, from /usr/include/boost/function/detail/prologue.hpp:17, @@ -941,25 +983,25 @@ ../src/FileUtils.cpp:163:62: note: returned from ‘void* operator new [](std::size_t)’ 163 | std::unique_ptr cwd(new char[chunkSize * chunks]); | ^ -[51/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FormatUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o -c ../src/FormatUtils.cpp -[52/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp -[53/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/IFastaWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o -c ../src/IFastaWriter.cpp +[52/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FormatUtils.cpp.o -MF src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o.d -o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o -c ../src/FormatUtils.cpp +[53/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp [54/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp -[55/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/IFastqWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o -c ../src/IFastqWriter.cpp -[56/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp -[57/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, @@ -983,8 +1025,8 @@ /usr/include/c++/12/bits/unique_ptr.h:395:19: warning: potential null pointer dereference [-Wnull-dereference] 395 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[70/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp -[71/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp +[71/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiBuilderBase.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o -c ../src/PbiBuilderBase.cpp +[72/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, @@ -1006,51 +1048,52 @@ /usr/include/c++/12/bits/unique_ptr.h:395:19: warning: potential null pointer dereference [-Wnull-dereference] 395 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[72/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp -[73/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp -[74/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.1.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.1.0.p/RecordType.cpp.o -c ../src/RecordType.cpp -[75/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o -c ../src/RunMetadata.cpp -[76/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp -[77/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[78/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp -[79/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/StringUtilities.cpp.o -MF src/libpbbam.so.2.1.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.2.1.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.cpp -[80/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.1.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.1.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp -[81/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.2.1.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.2.1.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp -[82/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.1.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/SamReader.cpp.o -c ../src/SamReader.cpp -[83/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.2.1.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.2.1.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp -[84/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/SamWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp -[85/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/TagCollection.cpp.o -MF src/libpbbam.so.2.1.0.p/TagCollection.cpp.o.d -o src/libpbbam.so.2.1.0.p/TagCollection.cpp.o -c ../src/TagCollection.cpp +[73/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp +[74/224] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra 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-Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp -[108/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp +[107/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp +[108/224] c++ -Isrc/libpbbam.so.2.1.0.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 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp -[112/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp -[113/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp +[110/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp +[111/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp +[112/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp +[113/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp [114/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp [115/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp -[116/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp +[116/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp +[117/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp +[118/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, @@ -1073,58 +1116,56 @@ /usr/include/c++/12/bits/unique_ptr.h:395:19: warning: potential null pointer dereference [-Wnull-dereference] 395 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[117/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp -[118/224] c++ -Isrc/libpbbam.so.2.1.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always 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-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp -[120/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp -[121/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp +[119/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC 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src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp -[124/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp -[125/224] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 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src/libpbbam.so.2.1.0.p/BamReader.cpp.o src/libpbbam.so.2.1.0.p/BamRecord.cpp.o src/libpbbam.so.2.1.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.1.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.1.0.p/BamRecordView.cpp.o src/libpbbam.so.2.1.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/BamWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.1.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.1.0.p/Compare.cpp.o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.1.0.p/Config.cpp.o src/libpbbam.so.2.1.0.p/DataSet.cpp.o src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o src/libpbbam.so.2.1.0.p/DataSetIO.cpp.o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.1.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.1.0.p/FaiIndex.cpp.o src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.1.0.p/MD5.cpp.o src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.1.0.p/PbiFile.cpp.o src/libpbbam.so.2.1.0.p/PbiFilter.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.1.0.p/PbiRawData.cpp.o src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.1.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.1.0.p/RecordType.cpp.o src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o src/libpbbam.so.2.1.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.1.0.p/SamReader.cpp.o src/libpbbam.so.2.1.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/SamWriter.cpp.o src/libpbbam.so.2.1.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.1.0.p/StringUtilities.cpp.o src/libpbbam.so.2.1.0.p/Tag.cpp.o src/libpbbam.so.2.1.0.p/TagCollection.cpp.o src/libpbbam.so.2.1.0.p/TextFileReader.cpp.o src/libpbbam.so.2.1.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.1.0.p/TimeUtils.cpp.o src/libpbbam.so.2.1.0.p/Validator.cpp.o src/libpbbam.so.2.1.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.1.0.p/ValidationException.cpp.o src/libpbbam.so.2.1.0.p/Version.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.1.0.p/XmlReader.cpp.o src/libpbbam.so.2.1.0.p/XmlWriter.cpp.o src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.1.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.1.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.1.0 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[130/224] /usr/bin/meson --internal symbolextractor /build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0.p/libpbbam.so.2.1.0.symbols -[131/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BedWriter.cpp.o -MF tests/pbbam_test.p/src_test_BedWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BedWriter.cpp.o -c ../tests/src/test_BedWriter.cpp -[132/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[133/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[123/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp +[124/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp +[125/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp +[126/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[127/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[128/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BedWriter.cpp.o -MF tests/pbbam_test.p/src_test_BedWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BedWriter.cpp.o -c ../tests/src/test_BedWriter.cpp +[129/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_BamWriter.cpp.o -MF tests/pbbam_test.p/src_test_BamWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BamWriter.cpp.o -c ../tests/src/test_BamWriter.cpp +[130/224] c++ -Isrc/libpbbam.so.2.1.0.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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.2.1.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.2.1.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.2.1.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp +[131/224] c++ -o src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamGitHash.cpp.o src/libpbbam.so.2.1.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.2.1.0.p/BaiIndexCache.cpp.o src/libpbbam.so.2.1.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.1.0.p/BamFile.cpp.o src/libpbbam.so.2.1.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.1.0.p/BamHeader.cpp.o src/libpbbam.so.2.1.0.p/BamReader.cpp.o src/libpbbam.so.2.1.0.p/BamRecord.cpp.o src/libpbbam.so.2.1.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.1.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.1.0.p/BamRecordView.cpp.o src/libpbbam.so.2.1.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/BamWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.1.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.1.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.1.0.p/Compare.cpp.o src/libpbbam.so.2.1.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.1.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.1.0.p/Config.cpp.o src/libpbbam.so.2.1.0.p/DataSet.cpp.o src/libpbbam.so.2.1.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetElement.cpp.o src/libpbbam.so.2.1.0.p/DataSetIO.cpp.o src/libpbbam.so.2.1.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.1.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.1.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.1.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.1.0.p/FaiIndex.cpp.o src/libpbbam.so.2.1.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.1.0.p/FastaCache.cpp.o src/libpbbam.so.2.1.0.p/FastaReader.cpp.o src/libpbbam.so.2.1.0.p/FastaSequence.cpp.o src/libpbbam.so.2.1.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.1.0.p/FastaWriter.cpp.o src/libpbbam.so.2.1.0.p/FastqReader.cpp.o src/libpbbam.so.2.1.0.p/FastqSequence.cpp.o src/libpbbam.so.2.1.0.p/FastqWriter.cpp.o src/libpbbam.so.2.1.0.p/FileProducer.cpp.o src/libpbbam.so.2.1.0.p/FileUtils.cpp.o src/libpbbam.so.2.1.0.p/FofnReader.cpp.o src/libpbbam.so.2.1.0.p/FormatUtils.cpp.o src/libpbbam.so.2.1.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.1.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.1.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.1.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.1.0.p/KSeqReader.cpp.o src/libpbbam.so.2.1.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.1.0.p/MD5.cpp.o src/libpbbam.so.2.1.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.1.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.1.0.p/PbiFile.cpp.o src/libpbbam.so.2.1.0.p/PbiFilter.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.1.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.1.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.1.0.p/PbiRawData.cpp.o src/libpbbam.so.2.1.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.1.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.1.0.p/RecordType.cpp.o src/libpbbam.so.2.1.0.p/RunMetadata.cpp.o src/libpbbam.so.2.1.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.1.0.p/SamReader.cpp.o src/libpbbam.so.2.1.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.1.0.p/SamWriter.cpp.o src/libpbbam.so.2.1.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.1.0.p/StringUtilities.cpp.o src/libpbbam.so.2.1.0.p/Tag.cpp.o src/libpbbam.so.2.1.0.p/TagCollection.cpp.o src/libpbbam.so.2.1.0.p/TextFileReader.cpp.o src/libpbbam.so.2.1.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.1.0.p/TimeUtils.cpp.o src/libpbbam.so.2.1.0.p/Validator.cpp.o src/libpbbam.so.2.1.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.1.0.p/ValidationException.cpp.o src/libpbbam.so.2.1.0.p/Version.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.1.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.1.0.p/XmlReader.cpp.o src/libpbbam.so.2.1.0.p/XmlWriter.cpp.o src/libpbbam.so.2.1.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.1.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.1.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.1.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.1.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.1.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.1.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.1.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.1.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.1.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.1.0 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[132/224] /usr/bin/meson --internal symbolextractor /build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0 src/libpbbam.so.2.1.0.p/libpbbam.so.2.1.0.symbols +[133/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [134/224] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always 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-D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_VcfReader.cpp.o -MF tests/pbbam_test.p/src_test_VcfReader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfReader.cpp.o -c ../tests/src/test_VcfReader.cpp +[180/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op 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-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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[183/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[184/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[185/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[186/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp +[183/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[184/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[185/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[186/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [187/224] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-2.1.0+dfsg/tests/data /build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/tests Generating test data in /build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/tests - Creating file: truncated.bam...done. @@ -1245,7 +1286,7 @@ - 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. -[188/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[188/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [189/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [190/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 /usr/include/c++/12/istream:39, @@ -1315,8 +1356,10 @@ 399 | float v2; | ^~ [191/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[192/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp -[193/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[192/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[193/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[194/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[195/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from /usr/include/c++/12/string:40, from ../tools/bam2sam/src/Bam2SamSettings.h:4, from ../tools/bam2sam/src/Bam2SamSettings.cpp:1: @@ -1330,19 +1373,16 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[194/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[195/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[196/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[197/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[196/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp +[197/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [198/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp -[199/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[200/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[199/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[200/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [201/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp [202/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [203/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [204/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[205/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp -[206/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_PbIndexDumpSettings.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp +[205/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_PbIndexDumpSettings.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp In file included from /usr/include/c++/12/string:40, from ../tools/pbindexdump/src/PbIndexDumpSettings.h:4, from ../tools/pbindexdump/src/PbIndexDumpSettings.cpp:1: @@ -1356,6 +1396,7 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets -4611686018427387902 and [-4611686018427387903, 4611686018427387904] may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +[206/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp [207/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp [208/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [209/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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_PbMergeSettings.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -c ../tools/pbmerge/src/PbMergeSettings.cpp @@ -1372,7 +1413,8 @@ /usr/include/c++/12/bits/char_traits.h:431:56: warning: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ accessing 9223372036854775810 or more bytes at offsets [2, 9223372036854775807] and 1 may overlap up to 9223372036854775813 bytes at offset -3 [-Wrestrict] 431 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -[210/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[210/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 +[211/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp In file included from /usr/include/c++/12/memory:76, from /usr/include/pbcopper/data/FrameEncoders.h:8, from ../include/pbbam/ReadGroupInfo.h:9, @@ -1394,14 +1436,13 @@ /usr/include/c++/12/bits/unique_ptr.h:395:19: warning: potential null pointer dereference [-Wnull-dereference] 395 | if (__ptr != nullptr) | ~~~~~~^~~~~~~~~~ -[211/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [212/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -[213/224] 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_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_QualityValues.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a -lpthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[214/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp -[215/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp -[216/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group -[217/224] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp -[218/224] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[213/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp +[214/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[215/224] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp +[216/224] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[217/224] 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_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_QualityValues.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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a /usr/lib/aarch64-linux-gnu/libgtest.a -lpthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group +[218/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [219/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 [220/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [221/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -1429,7 +1470,7 @@ | ~~~~~~^~~~~~~~~~ [224/224] 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/pbbam-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.1.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test -make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt binnengegaan sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ @@ -1563,7 +1604,7 @@ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${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 @@ -1574,7 +1615,7 @@ tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed # Ran 8 tests, 0 skipped, 0 failed. -make[1]: Leaving directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson @@ -1646,8 +1687,8 @@ 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.2.1.0 to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu Installing tools/bam2sam to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/bin @@ -1783,7 +1824,7 @@ Installing /build/pbbam-2.1.0+dfsg/obj-aarch64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig Installing symlink pointing to libpbbam.so.2.1.0 to /build/pbbam-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so debian/rules override_dh_install -make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt binnengegaan dh_install d-shlibmove --commit \ --multiarch \ @@ -1811,12 +1852,12 @@ install -d -m 755 debian/libpbbam-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/aarch64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete -make[1]: Leaving directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt verlaten dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs -make[1]: Entering directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt binnengegaan dh_installchangelogs CHANGELOG.md -make[1]: Leaving directory '/build/pbbam-2.1.0+dfsg' +make[1]: Map '/build/pbbam-2.1.0+dfsg' wordt verlaten dh_installsystemduser -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson @@ -1833,11 +1874,11 @@ dpkg-gencontrol: warning: package libpbbam-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_2.1.0+dfsg-2_arm64.deb'. -dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.1.0+dfsg-2_arm64.deb'. -dpkg-deb: building package 'libpbbam2.1.0' in '../libpbbam2.1.0_2.1.0+dfsg-2_arm64.deb'. -dpkg-deb: building package 'libpbbam2.1.0-dbgsym' in '../libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_arm64.deb'. -dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.1.0+dfsg-2_arm64.deb'. +dpkg-deb: pakket 'pbbamtools' wordt gebouwd in '../pbbamtools_2.1.0+dfsg-2_arm64.deb'. +dpkg-deb: pakket 'libpbbam2.1.0-dbgsym' wordt gebouwd in '../libpbbam2.1.0-dbgsym_2.1.0+dfsg-2_arm64.deb'. +dpkg-deb: pakket 'pbbamtools-dbgsym' wordt gebouwd in '../pbbamtools-dbgsym_2.1.0+dfsg-2_arm64.deb'. +dpkg-deb: pakket 'libpbbam-dev' wordt gebouwd in '../libpbbam-dev_2.1.0+dfsg-2_arm64.deb'. +dpkg-deb: pakket 'libpbbam2.1.0' wordt gebouwd in '../libpbbam2.1.0_2.1.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbbam_2.1.0+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../pbbam_2.1.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1845,12 +1886,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/18953/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18953/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/9386 and its subdirectories -I: Current time: Thu Apr 27 05:32:32 -12 2023 -I: pbuilder-time-stamp: 1682616752 +I: removing directory /srv/workspace/pbuilder/18953 and its subdirectories +I: Current time: Thu May 30 13:37:55 +14 2024 +I: pbuilder-time-stamp: 1717025875