Diff of the two buildlogs: -- --- b1/build.log 2025-03-17 20:59:34.955302185 +0000 +++ b2/build.log 2025-03-17 21:14:23.947486329 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 19 15:20:17 -12 2026 -I: pbuilder-time-stamp: 1776655217 +I: Current time: Tue Mar 18 10:59:37 +14 2025 +I: pbuilder-time-stamp: 1742245177 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/373445/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/516737/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 17 20:59 /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/516737/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/516737/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d2472a574b634ca2bf48a1696f3440c2' - 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='373445' - PS1='# ' - PS2='> ' + INVOCATION_ID=b96458d504bf407ba4685f22e0f2e0bd + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=516737 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.2mHi6IEd/pbuilderrc_fqmb --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2mHi6IEd/b1 --logfile b1/build.log blasr_5.3.5+dfsg-7.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.2mHi6IEd/pbuilderrc_M9gL --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2mHi6IEd/b2 --logfile b2/build.log blasr_5.3.5+dfsg-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/373445/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/516737/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -288,7 +320,7 @@ Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 meson all 1.7.0-1 [639 kB] -Fetched 88.6 MB in 2s (39.2 MB/s) +Fetched 88.6 MB in 10s (8874 kB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19803 files and directories currently installed.) @@ -803,8 +835,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 20 03:21:27 UTC 2026. -Universal Time is now: Mon Apr 20 03:21:27 UTC 2026. +Local time is now: Mon Mar 17 21:04:31 UTC 2025. +Universal Time is now: Mon Mar 17 21:04:31 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -944,7 +976,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/blasr-5.3.5+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 > ../blasr_5.3.5+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/516737/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/516737/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/blasr-5.3.5+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 > ../blasr_5.3.5+dfsg-7_source.changes dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -1005,16 +1041,12 @@ Found ninja-1.12.1 at /usr/bin/ninja make[1]: Leaving directory '/build/reproducible-path/blasr-5.3.5+dfsg' dh_auto_build -O--buildsystem=meson - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j42 -v + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j20 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h 5.3.5 /build/reproducible-path/blasr-5.3.5+dfsg @BLASR_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' -[2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp -[3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp -[4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp -[5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp -[6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp -[7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp -[8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp -[9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp +[2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp +[3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp +[4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp +[5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] @@ -1047,6 +1079,10 @@ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ +[6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp +[7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp +[8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp +[9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp [11/25] c++ -Isawriter.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ sawriter.p/utils_SAWriter.cpp.o -MF sawriter.p/utils_SAWriter.cpp.o.d -o sawriter.p/utils_SAWriter.cpp.o -c ../utils/SAWriter.cpp [12/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp @@ -1092,93 +1128,7 @@ /usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[13/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp -In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../utils/SamToM4.cpp:21: -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: -/usr/include/c++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ - 575 | __a.construct(__p, std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ - 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1289 | __x); - | ~~~~ -/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here - 112 | alignments.push_back(alignment); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: -/usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from ../utils/SamToM4.cpp:19: -/usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[14/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp -In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../utils/SDPMatcher.cpp:8: -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: -/usr/include/c++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ - 575 | __a.construct(__p, std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ - 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1289 | __x); - | ~~~~ -/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here - 112 | alignments.push_back(alignment); - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: -/usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/string:43, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from ../utils/SDPMatcher.cpp:3: -/usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[15/25] c++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp +[13/25] c++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, @@ -1255,7 +1205,50 @@ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ -[16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp +[14/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp +In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../utils/SamToM4.cpp:21: +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: +/usr/include/c++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ + 575 | __a.construct(__p, std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ + 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1289 | __x); + | ~~~~ +/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here + 112 | alignments.push_back(alignment); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: +/usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from ../utils/SamToM4.cpp:19: +/usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[15/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, @@ -1332,6 +1325,49 @@ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ +[16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp +In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../utils/SDPMatcher.cpp:8: +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: +/usr/include/c++/14/bits/alloc_traits.h:575:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ + 575 | __a.construct(__p, std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_vector.h:1288:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ + 1288 | _Alloc_traits::construct(this->_M_impl, this->_M_impl._M_finish, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1289 | __x); + | ~~~~ +/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here + 112 | alignments.push_back(alignment); + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: +/usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/string:43, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from ../utils/SDPMatcher.cpp:3: +/usr/include/c++/14/bits/new_allocator.h:191:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_GLIBCXX_ASSERTIONS=1 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/blasr-5.3.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: @@ -2236,8 +2272,8 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-7_amd64.deb'. dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.5+dfsg-7_amd64.deb'. +dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../blasr_5.3.5+dfsg-7_amd64.buildinfo dpkg-genchanges --build=binary -O../blasr_5.3.5+dfsg-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2245,12 +2281,14 @@ 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/516737/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/516737/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/373445 and its subdirectories -I: Current time: Sun Apr 19 15:22:34 -12 2026 -I: pbuilder-time-stamp: 1776655354 +I: removing directory /srv/workspace/pbuilder/516737 and its subdirectories +I: Current time: Tue Mar 18 11:14:23 +14 2025 +I: pbuilder-time-stamp: 1742246063