Diff of the two buildlogs: -- --- b1/build.log 2024-04-17 07:41:12.724814114 +0000 +++ b2/build.log 2024-04-17 07:44:15.309076181 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 16 19:38:36 -12 2024 -I: pbuilder-time-stamp: 1713339516 +I: Current time: Wed Apr 17 21:41:38 +14 2024 +I: pbuilder-time-stamp: 1713339698 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying pkg-config.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/14750/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27223/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 Apr 17 07:41 /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/27223/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27223/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='6361a15cc89947ef95b48bed396d771e' - 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='14750' - PS1='# ' - PS2='> ' + INVOCATION_ID=5c8bf6b643234b1a8a9450f3ed674445 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=27223 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.GMPVcTK8/pbuilderrc_AlNW --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.GMPVcTK8/b1 --logfile b1/build.log libseqlib_1.2.0+dfsg-11.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.GMPVcTK8/pbuilderrc_HPAg --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.GMPVcTK8/b2 --logfile b2/build.log libseqlib_1.2.0+dfsg-11.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 16 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/14750/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 15 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/27223/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -214,7 +246,7 @@ Get: 72 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf pkg-kde-tools all 0.15.38 [97.8 kB] -Fetched 29.6 MB in 1s (49.0 MB/s) +Fetched 29.6 MB in 1s (35.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19635 files and directories currently installed.) @@ -466,8 +498,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Apr 17 07:39:17 UTC 2024. -Universal Time is now: Wed Apr 17 07:39:17 UTC 2024. +Local time is now: Wed Apr 17 07:42:24 UTC 2024. +Universal Time is now: Wed Apr 17 07:42:24 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -533,7 +565,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libseqlib-1.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libseqlib_1.2.0+dfsg-11_source.changes +I: user script /srv/workspace/pbuilder/27223/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/27223/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libseqlib-1.2.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libseqlib_1.2.0+dfsg-11_source.changes dpkg-buildpackage: info: source package libseqlib dpkg-buildpackage: info: source version 1.2.0+dfsg-11 dpkg-buildpackage: info: source distribution unstable @@ -681,25 +717,33 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' Making all in src make[3]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FastqReader.lo `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BFC.lo `test -f 'BFC.cpp' || echo './'`BFC.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-ReadFilter.lo `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FastqReader.lo `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BFC.lo `test -f 'BFC.cpp' || echo './'`BFC.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-ReadFilter.lo `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-SeqPlot.lo `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -fPIC -DPIC -o .libs/libseqlib_la-ReadFilter.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -fPIC -DPIC -o .libs/libseqlib_la-BFC.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -o libseqlib_la-FastqReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -o libseqlib_la-BFC.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-SeqPlot.lo `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-GenomicRegion.lo `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-GenomicRegion.lo `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -fPIC -DPIC -o .libs/libseqlib_la-GenomicRegion.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-RefGenome.lo `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -o libseqlib_la-SeqPlot.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamWriter.lo `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamReader.lo `test -f 'BamReader.cpp' || echo './'`BamReader.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:72, from ../SeqLib/ReadFilter.h:7, from ReadFilter.cpp:1: @@ -718,8 +762,8 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-RefGenome.lo `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BWAWrapper.lo `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator]', inlined from 'SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const std::string&, const SeqLib::BamHeader&)' at ReadFilter.cpp:252:33: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -730,19 +774,6 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamWriter.lo `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamReader.lo `test -f 'BamReader.cpp' || echo './'`BamReader.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BWAWrapper.lo `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamRecord.lo `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o In file included from /usr/include/c++/13/vector:72, from ../SeqLib/BWAWrapper.h:5, from BWAWrapper.cpp:9: @@ -774,6 +805,7 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mem_aln_t; _Alloc = std::allocator]', inlined from 'void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const' at BWAWrapper.cpp:297:18: @@ -800,8 +832,12 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -o libseqlib_la-BWAWrapper.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FermiAssembler.lo `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamRecord.lo `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FermiAssembler.lo `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o In file included from /usr/include/c++/13/vector:72, from ../SeqLib/BamRecord.h:6, @@ -824,10 +860,10 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -o libseqlib_la-BamRecord.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -o libseqlib_la-FermiAssembler.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamHeader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -o libseqlib_la-BamHeader.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0 -lfml `/usr/bin/pkg-config --libs htslib` `/usr/bin/pkg-config --libs jsoncpp` -lssw -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/arm-linux-gnueabihf libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lbz2 -llzma -lz -pthread +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0 -lfml `/usr/bin/pkg-config --libs htslib` `/usr/bin/pkg-config --libs jsoncpp` -lssw -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/arm-linux-gnueabihf libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lbz2 -llzma -lz -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o .libs/libseqlib_la-FastqReader.o .libs/libseqlib_la-BFC.o .libs/libseqlib_la-ReadFilter.o .libs/libseqlib_la-SeqPlot.o .libs/libseqlib_la-GenomicRegion.o .libs/libseqlib_la-RefGenome.o .libs/libseqlib_la-BamWriter.o .libs/libseqlib_la-BamReader.o .libs/libseqlib_la-BWAWrapper.o .libs/libseqlib_la-BamRecord.o .libs/libseqlib_la-FermiAssembler.o .libs/libseqlib_la-BamHeader.o -lfml -lhts -ljsoncpp -lssw -lbz2 -llzma -lz -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libseqlib.so.2 -o .libs/libseqlib.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libseqlib.so.2" && ln -s "libseqlib.so.2.0.0" "libseqlib.so.2") libtool: link: (cd ".libs" && rm -f "libseqlib.so" && ln -s "libseqlib.so.2.0.0" "libseqlib.so") @@ -840,7 +876,7 @@ make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' @@ -902,16 +938,16 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: symbol kseq_read used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol err_fclose used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol err_fflush used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bns_destroy used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol bwt_bwtupdate_core used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol mem_reg2aln used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwt_dump_bwt used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol bwt_dump_sa used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_xopen_core used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol err_fflush used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol bwt_cal_sa used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol nst_nt4_table used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol kseq_init used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol kseq_read used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol mem_align1 used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol bwa_idx_destroy used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol @@ -927,12 +963,14 @@ 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/27223/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27223/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/14750 and its subdirectories -I: Current time: Tue Apr 16 19:41:08 -12 2024 -I: pbuilder-time-stamp: 1713339668 +I: removing directory /srv/workspace/pbuilder/27223 and its subdirectories +I: Current time: Wed Apr 17 21:44:10 +14 2024 +I: pbuilder-time-stamp: 1713339850