Diff of the two buildlogs: -- --- b1/build.log 2024-05-06 14:27:55.909318225 +0000 +++ b2/build.log 2024-05-06 14:29:09.282197802 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 02:26:46 -12 2024 -I: pbuilder-time-stamp: 1715005606 +I: Current time: Mon Jun 9 10:50:59 +14 2025 +I: pbuilder-time-stamp: 1749415859 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying CVE-2021-42006.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1288387/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2789682/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 8 20:51 /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/2789682/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2789682/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a7e7f6dda26d49afb03f87e7495ea7fb' - 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='1288387' - PS1='# ' - PS2='> ' + INVOCATION_ID=69ffc87c457f46a9882542f38db9eb48 + 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=2789682 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.QioX2H7t/pbuilderrc_IzoY --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.QioX2H7t/b1 --logfile b1/build.log libgclib_0.12.7+ds-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QioX2H7t/pbuilderrc_EhtC --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.QioX2H7t/b2 --logfile b2/build.log libgclib_0.12.7+ds-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:23 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1288387/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2789682/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -143,7 +175,7 @@ Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (122 MB/s) +Fetched 18.7 MB in 0s (140 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19743 files and directories currently installed.) @@ -282,7 +314,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes +I: user script /srv/workspace/pbuilder/2789682/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2789682/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgclib-0.12.7+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgclib_0.12.7+ds-5_source.changes dpkg-buildpackage: info: source package libgclib dpkg-buildpackage: info: source version 0.12.7+ds-5 dpkg-buildpackage: info: source distribution unstable @@ -335,8 +371,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking build system type... aarch64-unknown-linux-gnu @@ -440,29 +476,28 @@ make all-am make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o mdtest.o mdtest.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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-Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-codons.lo `test -f 'codons.cpp' || echo './'`codons.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GAlnExtend.lo `test -f 'GAlnExtend.cpp' || echo './'`GAlnExtend.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GapAssem.lo `test -f 'GapAssem.cpp' || echo './'`GapAssem.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GArgs.lo `test -f 'GArgs.cpp' || echo './'`GArgs.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GBase.lo `test -f 'GBase.cpp' || echo './'`GBase.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gcdb.lo `test -f 'gcdb.cpp' || echo './'`gcdb.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GCdbYank.lo `test -f 'GCdbYank.cpp' || echo './'`GCdbYank.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gdna.lo `test -f 'gdna.cpp' || echo './'`gdna.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFaSeqGet.lo `test -f 'GFaSeqGet.cpp' || echo './'`GFaSeqGet.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GFastaIndex.lo `test -f 'GFastaIndex.cpp' || echo './'`GFastaIndex.cpp +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gff.lo `test -f 'gff.cpp' || echo './'`gff.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -fPIC -DPIC -o .libs/libgclib_la-GBase.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -fPIC -DPIC -o .libs/libgclib_la-GAlnExtend.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -fPIC -DPIC -o .libs/libgclib_la-GapAssem.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -fPIC -DPIC -o .libs/libgclib_la-codons.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -fPIC -DPIC -o .libs/libgclib_la-GArgs.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -fPIC -DPIC -o .libs/libgclib_la-gcdb.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -fPIC -DPIC -o .libs/libgclib_la-gdna.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -fPIC -DPIC -o .libs/libgclib_la-GFastaIndex.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -fPIC -DPIC -o .libs/libgclib_la-gff.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -fPIC -DPIC -o .libs/libgclib_la-GCdbYank.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -fPIC -DPIC -o .libs/libgclib_la-GFaSeqGet.o -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp gcdb.cpp: In function ‘unsigned int gcdb_strlen(const char*)’: gcdb.cpp:102:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 102 | register char *t; @@ -475,26 +510,12 @@ gcdb.cpp:843:13: warning: comparing the result of pointer addition ‘(x + 1)’ and NULL [-Waddress] 843 | if (x + 1) { | ~~^~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gsocket.lo `test -f 'gsocket.cpp' || echo './'`gsocket.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c codons.cpp -o libgclib_la-codons.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -fPIC -DPIC -o .libs/libgclib_la-gsocket.o -In file included from GFastaFile.h:4, - from GapAssem.h:3, - from GapAssem.cpp:1: -GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: -GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] - 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ - | ^~ -GapAssem.cpp:236:14: note: ‘gxpos’ was declared here - 236 | int* gxpos; //mapping of positions from gseq to seq - | ^~~~~ -GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] - 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ - | ^~ -GapAssem.cpp:212:15: note: ‘gseq’ was declared here - 212 | char* gseq; - | ^~~~ GAlnExtend.cpp: In function ‘color_fg(int, _IO_FILE*)’: GAlnExtend.cpp:13:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 13 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+30); @@ -518,7 +539,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GCdbYank.cpp -o libgclib_la-GCdbYank.o >/dev/null 2>&1 GAlnExtend.cpp: In function ‘color_bg(int, _IO_FILE*)’: GAlnExtend.cpp:19:35: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=] 19 | sprintf((char *)(&COLOR_buf[2]),"%dm",c+40); @@ -538,14 +558,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-gstopwatch.lo `test -f 'gstopwatch.cpp' || echo './'`gstopwatch.cpp -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gcdb.cpp -o libgclib_la-gcdb.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gdna.cpp -o libgclib_la-gdna.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GArgs.cpp -o libgclib_la-GArgs.o >/dev/null 2>&1 In file included from gff.cpp:1: gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { @@ -562,14 +576,37 @@ gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 gff.cpp: In constructor ‘GffLine::GffLine(GffReader*, const char*)’: gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from GFastaFile.h:4, + from GapAssem.h:3, + from GapAssem.cpp:1: +GapAssem.cpp: In member function ‘GASeq::refineClipping(GDynArray&, int, bool)’: +GBase.h:176:28: warning: ‘gxpos’ may be used uninitialized [-Wmaybe-uninitialized] + 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ + | ^~ +GapAssem.cpp:236:14: note: ‘gxpos’ was declared here + 236 | int* gxpos; //mapping of positions from gseq to seq + | ^~~~~ +GBase.h:176:28: warning: ‘gseq’ may be used uninitialized [-Wmaybe-uninitialized] + 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ + | ^~ +GapAssem.cpp:212:15: note: ‘gseq’ was declared here + 212 | char* gseq; + | ^~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -fPIC -DPIC -o .libs/libgclib_la-gstopwatch.o +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GStr.lo `test -f 'GStr.cpp' || echo './'`GStr.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gsocket.cpp -o libgclib_la-gsocket.o >/dev/null 2>&1 +/bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c -o libgclib_la-GThreads.lo `test -f 'GThreads.cpp' || echo './'`GThreads.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GBase.cpp -o libgclib_la-GBase.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFastaIndex.cpp -o libgclib_la-GFastaIndex.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -fPIC -DPIC -o .libs/libgclib_la-GStr.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gstopwatch.cpp -o libgclib_la-gstopwatch.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -fPIC -DPIC -o .libs/libgclib_la-GThreads.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GThreads.cpp -o libgclib_la-GThreads.o >/dev/null 2>&1 In file included from GStr.h:5, from GStr.cpp:2: @@ -580,8 +617,7 @@ GStr.cpp:38:15: note: ‘data’ was declared here 38 | Data* data; | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GFaSeqGet.cpp -o libgclib_la-GFaSeqGet.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GAlnExtend.cpp -o libgclib_la-GAlnExtend.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GapAssem.cpp -o libgclib_la-GapAssem.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp -o libgclib_la-GStr.o >/dev/null 2>&1 In file included from gff.h:6: gff.cpp: In member function ‘BEDLine::BEDLine(GffReader*, char const*)’: @@ -592,7 +628,7 @@ 242 | char** bstart; | ^~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -c gff.cpp -o libgclib_la-gff.o >/dev/null 2>&1 -/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo +/bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -version-info 3:0 -lpthread -Wl,-z,relro -Wl,-z,now -Wl,-flto -o libgclib.la -rpath /usr/lib/aarch64-linux-gnu libgclib_la-codons.lo libgclib_la-GAlnExtend.lo libgclib_la-GapAssem.lo libgclib_la-GArgs.lo libgclib_la-GBase.lo libgclib_la-gcdb.lo libgclib_la-GCdbYank.lo libgclib_la-gdna.lo libgclib_la-GFaSeqGet.lo libgclib_la-GFastaIndex.lo libgclib_la-gff.lo libgclib_la-gsocket.lo libgclib_la-gstopwatch.lo libgclib_la-GStr.lo libgclib_la-GThreads.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/crtbeginS.o .libs/libgclib_la-codons.o .libs/libgclib_la-GAlnExtend.o .libs/libgclib_la-GapAssem.o .libs/libgclib_la-GArgs.o .libs/libgclib_la-GBase.o .libs/libgclib_la-gcdb.o .libs/libgclib_la-GCdbYank.o .libs/libgclib_la-gdna.o .libs/libgclib_la-GFaSeqGet.o .libs/libgclib_la-GFastaIndex.o .libs/libgclib_la-gff.o .libs/libgclib_la-gsocket.o .libs/libgclib_la-gstopwatch.o .libs/libgclib_la-GStr.o .libs/libgclib_la-GThreads.o -lpthread -L/usr/lib/gcc/aarch64-linux-gnu/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -flto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -Wl,-soname -Wl,libgclib.so.3 -o .libs/libgclib.so.3.0.0 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information @@ -620,7 +656,7 @@ libtool: link: ar cr .libs/libgclib.a libgclib_la-codons.o libgclib_la-GAlnExtend.o libgclib_la-GapAssem.o libgclib_la-GArgs.o libgclib_la-GBase.o libgclib_la-gcdb.o libgclib_la-GCdbYank.o libgclib_la-gdna.o libgclib_la-GFaSeqGet.o libgclib_la-GFastaIndex.o libgclib_la-gff.o libgclib_la-gsocket.o libgclib_la-gstopwatch.o libgclib_la-GStr.o libgclib_la-GThreads.o libtool: link: ranlib .libs/libgclib.a libtool: link: ( cd ".libs" && rm -f "libgclib.la" && ln -s "../libgclib.la" "libgclib.la" ) -/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la +/bin/sh ./libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z,relro -Wl,-z,now -Wl,-flto -o mdtest mdtest.o libgclib.la libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgclib-0.12.7+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -flto -ffat-lto-objects -fPIC -D_FILE_OFFSET_BITS=64 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-flto -o .libs/mdtest mdtest.o ./.libs/libgclib.so make[2]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' make[1]: Leaving directory '/build/reproducible-path/libgclib-0.12.7+ds' @@ -641,7 +677,7 @@ make[1]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' make[2]: Entering directory '/build/reproducible-path/libgclib-0.12.7+ds' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ./libtool --mode=install /usr/bin/install -c libgclib.la '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgclib.so.3.0.0 /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.so.3.0.0 libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so.3 || { rm -f libgclib.so.3 && ln -s libgclib.so.3.0.0 libgclib.so.3; }; }) libtool: install: (cd /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libgclib.so.3.0.0 libgclib.so || { rm -f libgclib.so && ln -s libgclib.so.3.0.0 libgclib.so; }; }) @@ -651,7 +687,7 @@ libtool: install: ranlib /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgclib.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' - /bin/bash ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' + /bin/sh ./libtool --mode=install /usr/bin/install -c mdtest '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin' libtool: warning: 'libgclib.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/mdtest /build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/bin/mdtest /usr/bin/mkdir -p '/build/reproducible-path/libgclib-0.12.7+ds/debian/tmp/usr/include' @@ -722,12 +758,14 @@ 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/2789682/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2789682/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/1288387 and its subdirectories -I: Current time: Mon May 6 02:27:54 -12 2024 -I: pbuilder-time-stamp: 1715005674 +I: removing directory /srv/workspace/pbuilder/2789682 and its subdirectories +I: Current time: Mon Jun 9 10:52:08 +14 2025 +I: pbuilder-time-stamp: 1749415928