Diff of the two buildlogs: -- --- b1/build.log 2024-12-20 09:11:39.874178734 +0000 +++ b2/build.log 2024-12-20 09:17:03.375456196 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 22 03:33:44 -12 2026 -I: pbuilder-time-stamp: 1769096024 +I: Current time: Fri Dec 20 23:11:47 +14 2024 +I: pbuilder-time-stamp: 1734685907 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,86 @@ dpkg-source: info: applying fix_pkg-config.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28409/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/9333/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 Dec 20 09:12 /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/9333/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/9333/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e3106e90b0f249f6833aac2cf7fd5012' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='28409' - PS1='# ' - PS2='> ' + INVOCATION_ID=08f874ed8b93438fa96ad15eac2a916e + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=9333 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.ePnhc9iM/pbuilderrc_t3jQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ePnhc9iM/b1 --logfile b1/build.log libgkarrays_2.1.0+dfsg-4.2.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.ePnhc9iM/pbuilderrc_WQRw --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ePnhc9iM/b2 --logfile b2/build.log libgkarrays_2.1.0+dfsg-4.2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28409/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/9333/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +179,7 @@ Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.22 [919 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 21.0 MB in 0s (93.0 MB/s) +Fetched 21.0 MB in 3s (6085 kB/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 ... 19953 files and directories currently installed.) @@ -285,7 +318,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libgkarrays_2.1.0+dfsg-4.2_source.changes +I: user script /srv/workspace/pbuilder/9333/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/9333/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libgkarrays_2.1.0+dfsg-4.2_source.changes dpkg-buildpackage: info: source package libgkarrays dpkg-buildpackage: info: source version 2.1.0+dfsg-4.2 dpkg-buildpackage: info: source distribution unstable @@ -502,7 +539,7 @@ config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/libProgressBar-1.2.0 (/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0) -configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=i686-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/i386-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=i686-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=. +configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/i386-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=i686-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' 'LDFLAGS=-Wl,-z,relro -Wl,-z,now' 'CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p @@ -646,7 +683,7 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j6 + make -j10 make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' Making all in src make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' @@ -665,17 +702,17 @@ make all-am make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o testPB.o testPB.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c -o progressBar.lo progressBar.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -fPIC -DPIC -o .libs/progressBar.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O6 -Wall --pedantic --ansi -c progressBar.cpp -o progressBar.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/i386-linux-gnu progressBar.lo +/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -version-info 1:2:1 -Wl,-z,relro -Wl,-z,now -o libProgressBar.la -rpath /usr/lib/i386-linux-gnu progressBar.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/14/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/i686-linux-gnu/14 -L/usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/14/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crtn.o -O6 -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libProgressBar.so.0 -o .libs/libProgressBar.so.0.1.2 libtool: link: (cd ".libs" && rm -f "libProgressBar.so.0" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so.0") libtool: link: (cd ".libs" && rm -f "libProgressBar.so" && ln -s "libProgressBar.so.0.1.2" "libProgressBar.so") libtool: link: ar cr .libs/libProgressBar.a progressBar.o libtool: link: ranlib .libs/libProgressBar.a libtool: link: ( cd ".libs" && rm -f "libProgressBar.la" && ln -s "../libProgressBar.la" "libProgressBar.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -lProgressBar -Wl,-z,relro -Wl,-z,now -o testProgressBar testPB.o libProgressBar.la +/bin/sh ../libtool --tag=CXX --mode=link g++ -O6 -Wall --pedantic --ansi -lProgressBar -Wl,-z,relro -Wl,-z,now -o testProgressBar testPB.o libProgressBar.la libtool: link: g++ -O6 -Wall --pedantic --ansi -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testProgressBar testPB.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libProgressBar.so make[5]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' @@ -685,16 +722,24 @@ make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buildTables.o buildTables.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArrays.lo gkArrays.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o solArray.lo solArray.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.lo utils.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArraysBuilder.lo gkArraysBuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArrays.lo gkArrays.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o solArray.lo solArray.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.lo utils.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 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-Wformat -Werror=format-security -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readsReader.lo readsReader.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o largebinvect.lo largebinvect.cxx +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -fPIC -DPIC -o .libs/gkArrays.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -fPIC -DPIC -o .libs/gkSABuilder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -fPIC -DPIC -o .libs/gkIFABuilder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -fPIC -DPIC -o .libs/utils.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -fPIC -DPIC -o .libs/largebinvect.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -fPIC -DPIC -o .libs/solArray.o In file included from ./readsReader.h:109, from ./gkArrays.h:115, from buildTables.cpp:111: @@ -707,11 +752,25 @@ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1 gkSABuilder.cpp: In function 'int64_t gkarrays::partition(SolArray*, SolArray*, uintSA, uintSA, uintSA)': gkSABuilder.cpp:340:24: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 340 | while(i <= end && values->get(i) < pivotv||((pivotv==values->get(i)) &&(pivotp>sa->get(i)))); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./readsReader.h:109, + from ./gkArrays.h:115, + from ./gkSABuilder.h:108, + from gkSABuilder.cpp:104: +./readsReader.h: At global scope: +./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] + 169 | static int kseq_read(kseq_t *seq) \ + | ^~~~~~~~~ +./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' + 227 | __KSEQ_READ + | ^~~~~~~~~~~ +./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' + 111 | KSEQ_INIT(gzFile, gzread) + | ^~~~~~~~~ In file included from readsReader.h:109, from gkArrays.h:115, from gkArraysBuilder.h:105, @@ -725,25 +784,22 @@ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -In file included from ./readsReader.h:109, - from ./gkArrays.h:115, - from ./gkSABuilder.h:108, - from gkSABuilder.cpp:104: -./readsReader.h: At global scope: -./kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] +In file included from readsReader.h:109, + from gkArrays.h:115, + from gkArrays.cpp:113: +kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ -./kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' +kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' 227 | __KSEQ_READ | ^~~~~~~~~~~ -./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' +readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1 In file included from readsReader.h:109, from gkArrays.h:115, - from gkArrays.cpp:113: + from gkCFPSBuilder.cpp:110: kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -753,8 +809,9 @@ readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkCFPSBuilder.lo gkCFPSBuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitvector.lo bitvector.cxx +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c utils.cpp -o utils.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c solArray.cpp -o solArray.o >/dev/null 2>&1 gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTagFactor(uint, uint, uint)': gkArrays.cpp:454:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation] 454 | strncpy(&final_dna[previous_length], dna, 4); @@ -762,9 +819,6 @@ gkArrays.cpp:460:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation] 460 | strncpy(&final_dna[previous_length], dna, (p+fact_length+readPos)%4); | ^ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -fPIC -DPIC -o .libs/gkCFPSBuilder.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readsReader.lo readsReader.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -fPIC -DPIC -o .libs/gkIFABuilder.o gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTag(uint)': gkArrays.cpp:425:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 4 bytes from a string of length 4 [-Wstringop-truncation] 425 | strncpy(&final_dna[previous_length], dna, 4); @@ -772,8 +826,7 @@ gkArrays.cpp:430:14: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying between 0 and 3 bytes from a string of length 4 [-Wstringop-truncation] 430 | strncpy(&final_dna[previous_length], dna, nextReadPos%4); | ^ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o largebinvect.lo largebinvect.cxx -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o In file included from ./readsReader.h:109, from ./gkArrays.h:115, from ./gkIFABuilder.h:107, @@ -787,30 +840,12 @@ ./readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -fPIC -DPIC -o .libs/largebinvect.o -In file included from readsReader.h:109, - from gkArrays.h:115, - from gkCFPSBuilder.cpp:110: -kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] - 169 | static int kseq_read(kseq_t *seq) \ - | ^~~~~~~~~ -kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ' - 227 | __KSEQ_READ - | ^~~~~~~~~~~ -readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' - 111 | KSEQ_INIT(gzFile, gzread) - | ^~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c largebinvect.cxx -o largebinvect.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -o readsReader.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rank9b.lo `test -f 'sux/rank9b.cpp' || echo './'`sux/rank9b.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkCFPSBuilder.cpp -o gkCFPSBuilder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitvector.lo bitvector.cxx -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -o gkIFABuilder.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -fPIC -DPIC -o .libs/bitvector.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rank9b.lo `test -f 'sux/rank9b.cpp' || echo './'`sux/rank9b.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1 sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)': sux/rank9b.cpp:144:100: warning: suggest parentheses around '-' inside '>>' [-Wparentheses] 144 | return counts[ block ] + ( counts[ block + 1 ] >> ( offset + ( offset >> sizeof offset * 8 - 4 & 0x8 ) ) * 9 & 0x1FF ) + count( bits[ word ] & ( ( 1ULL << k % 64 ) - 1 ) ); @@ -819,15 +854,17 @@ sux/rank9b.cpp:207:88: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 207 | const uint64_t rank_in_word = rank_in_block - ( subcounts >> ( offset_in_block - 1 & 7 ) * 9 & 0x1FF ); | ~~~~~~~~~~~~~~~~^~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkIFABuilder.cpp -o gkIFABuilder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkSABuilder.cpp -o gkSABuilder.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/14/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -Wl,-rpath -Wl,/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so -lpthread -lz -L/usr/lib/gcc/i686-linux-gnu/14 -L/usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/14/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: link: (cd ".libs" && rm -f "libGkArrays.so.1" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so.1") libtool: link: (cd ".libs" && rm -f "libGkArrays.so" && ln -s "libGkArrays.so.1.1.0" "libGkArrays.so") libtool: link: ar cr .libs/libGkArrays.a gkArrays.o solArray.o utils.o gkArraysBuilder.o gkSABuilder.o gkCFPSBuilder.o gkIFABuilder.o readsReader.o largebinvect.o bitvector.o rank9b.o libtool: link: ranlib .libs/libGkArrays.a libtool: link: ( cd ".libs" && rm -f "libGkArrays.la" && ln -s "../libGkArrays.la" "libGkArrays.la" ) -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o buildTables buildTables.o libGkArrays.la -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/buildTables buildTables.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libGkArrays.so -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' @@ -840,7 +877,7 @@ make[2]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' dh_auto_test - make -j6 check "TESTSUITEFLAGS=-j6 --verbose" VERBOSE=1 + make -j10 check "TESTSUITEFLAGS=-j10 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' @@ -875,9 +912,9 @@ g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o checkPairedEnd.o checkPairedEnd.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o testVariableFixed.o testVariableFixed.cpp g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o testConsistency.o testConsistency.cpp +g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o checkConsistency.o checkConsistency.cpp In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, - from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115, - from compareVariableFixed.cpp:109: + from checkPairedEnd.cpp:104: /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -888,7 +925,8 @@ 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, - from checkPairedEnd.cpp:104: + from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115, + from compareVariableFixed.cpp:109: /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 169 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ @@ -898,9 +936,7 @@ /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../config -I/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src -DDATADIR=\"./\" -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o checkConsistency.o checkConsistency.cpp -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz -libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testPairedEnd testPairedEnd.o checkPairedEnd.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz In file included from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:109, from /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/gkArrays.h:115, from checkConsistency.cpp:104: @@ -913,11 +949,12 @@ /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT' 111 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testVariableFixed testVariableFixed.o compareVariableFixed.o -lpthread -lz +libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testPairedEnd testPairedEnd.o checkPairedEnd.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/variableAndFixedLength variableAndFixedLength.o compareVariableFixed.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testVariableFixed testVariableFixed.o compareVariableFixed.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testConsistency testConsistency.o checkConsistency.o -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/testConsistency testConsistency.o checkConsistency.o /build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/tests' make check-TESTS @@ -973,7 +1010,7 @@ make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[5]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' /usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libProgressBar.so.0.1.2 libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so.0 || { rm -f libProgressBar.so.0 && ln -s libProgressBar.so.0.1.2 libProgressBar.so.0; }; }) libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libProgressBar.so.0.1.2 libProgressBar.so || { rm -f libProgressBar.so && ln -s libProgressBar.so.0.1.2 libProgressBar.so; }; }) @@ -1007,9 +1044,9 @@ make[3]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' make[4]: Entering directory '/build/reproducible-path/libgkarrays-2.1.0+dfsg/src' /usr/bin/mkdir -p '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu' libtool: warning: relinking 'libGkArrays.la' -libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/src; /bin/bash "/build/reproducible-path/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp) +libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/src; /bin/sh "/build/reproducible-path/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar -Wl,-z,relro -Wl,-z,now -o libGkArrays.la -rpath /usr/lib/i386-linux-gnu gkArrays.lo solArray.lo utils.lo gkArraysBuilder.lo gkSABuilder.lo gkCFPSBuilder.lo gkIFABuilder.lo readsReader.lo largebinvect.lo bitvector.lo rank9b.lo -lpthread -lz -inst-prefix-dir /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/14/crtbeginS.o .libs/gkArrays.o .libs/solArray.o .libs/utils.o .libs/gkArraysBuilder.o .libs/gkSABuilder.o .libs/gkCFPSBuilder.o .libs/gkIFABuilder.o .libs/readsReader.o .libs/largebinvect.o .libs/bitvector.o .libs/rank9b.o -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu -L/usr/lib/i386-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/i686-linux-gnu/14 -L/usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/14/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libGkArrays.so.1 -o .libs/libGkArrays.so.1.1.0 libtool: install: /usr/bin/install -c .libs/libGkArrays.so.1.1.0T /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libGkArrays.so.1.1.0 libtool: install: (cd /build/reproducible-path/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libGkArrays.so.1.1.0 libGkArrays.so.1 || { rm -f libGkArrays.so.1 && ln -s libGkArrays.so.1.1.0 libGkArrays.so.1; }; }) @@ -1119,12 +1156,14 @@ 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/9333/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/9333/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/28409 and its subdirectories -I: Current time: Thu Jan 22 03:34:38 -12 2026 -I: pbuilder-time-stamp: 1769096078 +I: removing directory /srv/workspace/pbuilder/9333 and its subdirectories +I: Current time: Fri Dec 20 23:17:01 +14 2024 +I: pbuilder-time-stamp: 1734686221