Diff of the two buildlogs: -- --- b1/build.log 2023-04-28 14:31:18.037206183 +0000 +++ b2/build.log 2023-04-28 14:33:01.260636930 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 30 08:52:30 -12 2024 -I: pbuilder-time-stamp: 1717102350 +I: Current time: Sat Apr 29 04:31:21 +14 2023 +I: pbuilder-time-stamp: 1682692281 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libgkarrays_2.1.0+dfsg.orig.tar.xz] I: copying [./libgkarrays_2.1.0+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 18 21:46:25 2020 -12 +gpgv: Signature made Thu Nov 19 23:46:25 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,52 +29,84 @@ 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/2778/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/11956/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 29 04:31 /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/11956/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/11956/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2778' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=11956 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.xZ8y7uLP/pbuilderrc_GMj0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xZ8y7uLP/b1 --logfile b1/build.log libgkarrays_2.1.0+dfsg-4.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.xZ8y7uLP/pbuilderrc_EwzB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xZ8y7uLP/b2 --logfile b2/build.log --extrapackages usrmerge libgkarrays_2.1.0+dfsg-4.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 30 04:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2778/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 27 00:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/11956/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 30 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 19.3 MB in 2s (11.6 MB/s) +Fetched 19.3 MB in 0s (53.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) @@ -288,8 +320,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_source.changes +I: user script /srv/workspace/pbuilder/11956/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/11956/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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_source.changes dpkg-buildpackage: info: source package libgkarrays dpkg-buildpackage: info: source version 2.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -506,7 +547,7 @@ config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/libProgressBar-1.2.0 (/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0) -configure: running /bin/bash ./configure --disable-option-checking '--prefix=/usr' '--build=aarch64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/aarch64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=aarch64-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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=aarch64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/aarch64-linux-gnu' '--runstatedir=/run' '--disable-maintainer-mode' '--disable-dependency-tracking' 'build_alias=aarch64-linux-gnu' 'CXXFLAGS=-g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 @@ -669,17 +710,17 @@ make all-am make[5]: Entering directory '/build/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/aarch64-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/aarch64-linux-gnu progressBar.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o .libs/progressBar.o -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-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/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libProgressBar.so make[5]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[4]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' @@ -689,20 +730,20 @@ make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0' make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -fPIC -DPIC -o .libs/gkArrays.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkArraysBuilder.lo gkArraysBuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkSABuilder.lo gkSABuilder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gkIFABuilder.lo gkIFABuilder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -fPIC -DPIC -o .libs/gkArraysBuilder.o In file included from ./readsReader.h:109, from ./gkArrays.h:115, from buildTables.cpp:111: @@ -719,24 +760,24 @@ 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] +In file included from readsReader.h:109, + from gkArrays.h:115, + from gkArraysBuilder.h:105, + from gkArraysBuilder.cpp:103: +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) | ^~~~~~~~~ In file included from ./readsReader.h:109, from ./gkArrays.h:115, - from ./gkIFABuilder.h:107, - from gkIFABuilder.cpp:105: + 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) \ | ^~~~~~~~~ @@ -746,6 +787,7 @@ ./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/libgkarrays-2.1.0+dfsg -I/build/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/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 gkCFPSBuilder.cpp:110: @@ -758,24 +800,24 @@ 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 gkArrays.cpp:113: -kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1 +In file included from ./readsReader.h:109, + from ./gkArrays.h:115, + from ./gkIFABuilder.h:107, + from gkIFABuilder.cpp:105: +./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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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 gkArraysBuilder.h:105, - from gkArraysBuilder.cpp:103: + 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) \ | ^~~~~~~~~ @@ -785,8 +827,8 @@ 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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArraysBuilder.cpp -o gkArraysBuilder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o gkArrays.cpp: In member function 'char* gkarrays::gkArrays::getTagFactor(uint, uint, uint)': gkArrays.cpp:454:14: warning: 'char* __builtin_strncpy(char*, const char*, long 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); @@ -801,15 +843,13 @@ gkArrays.cpp:430:14: warning: 'char* __builtin_strncpy(char*, const char*, long 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); | ^ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -fPIC -DPIC -o .libs/readsReader.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o largebinvect.lo 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--tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c gkArrays.cpp -o gkArrays.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -fPIC -DPIC -o .libs/rank9b.o sux/rank9b.cpp: In member function 'uint64_t rank9b::rank(uint64_t)': sux/rank9b.cpp:144:100: warning: suggest parentheses around '-' inside '>>' [-Wparentheses] @@ -819,19 +859,20 @@ 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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readsReader.cpp -o readsReader.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c bitvector.cxx -o bitvector.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c sux/rank9b.cpp -o rank9b.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../config -I/build/libgkarrays-2.1.0+dfsg -I/build/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/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/libgkarrays-2.1.0+dfsg -I/build/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/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=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/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/aarch64-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/libgkarrays-2.1.0+dfsg -I/build/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/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=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/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/aarch64-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/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/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/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so -lpthread -lz -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -lpthread -L/build/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/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/libgkarrays-2.1.0+dfsg/src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs /build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs/libProgressBar.so ./.libs/libGkArrays.so -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' make[2]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/src' @@ -915,13 +956,13 @@ /build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -Wl,-z,relro -Wl,-z,now -o testPairedEnd testPairedEnd.o checkPairedEnd.o -lpthread -lz +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/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/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/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/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/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/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -L/build/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/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/libgkarrays-2.1.0+dfsg/tests/../src/.libs/libGkArrays.so -L/build/libgkarrays-2.1.0+dfsg/tests/../src/.libs -lpthread -lz make[3]: Leaving directory '/build/libgkarrays-2.1.0+dfsg/tests' make check-TESTS @@ -977,7 +1018,7 @@ make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' make[5]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar' /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libProgressBar.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libProgressBar.so.0.1.2 /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libProgressBar.so.0.1.2 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-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/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-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; }; }) @@ -1011,9 +1052,9 @@ make[3]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' make[4]: Entering directory '/build/libgkarrays-2.1.0+dfsg/src' /usr/bin/mkdir -p '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libGkArrays.la '/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: warning: relinking 'libGkArrays.la' -libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/src; /bin/bash "/build/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/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/aarch64-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/libgkarrays-2.1.0+dfsg/debian/tmp) +libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/src; /bin/sh "/build/libgkarrays-2.1.0+dfsg/libtool" --tag CXX --mode=relink g++ -g -O2 -ffile-prefix-map=/build/libgkarrays-2.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0:1 -lpthread -L/build/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/aarch64-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/libgkarrays-2.1.0+dfsg/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/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/libgkarrays-2.1.0+dfsg/src/libProgressBar-1.2.0/libProgressBar/.libs -L/build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -lProgressBar -lpthread -lz -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-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/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libGkArrays.so.1.1.0 libtool: install: (cd /build/libgkarrays-2.1.0+dfsg/debian/tmp/usr/lib/aarch64-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; }; }) @@ -1112,8 +1153,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libgkarrays1-dbgsym' in '../libgkarrays1-dbgsym_2.1.0+dfsg-4_arm64.deb'. -dpkg-deb: building package 'libgkarrays1' in '../libgkarrays1_2.1.0+dfsg-4_arm64.deb'. dpkg-deb: building package 'libgkarrays-dev' in '../libgkarrays-dev_2.1.0+dfsg-4_arm64.deb'. +dpkg-deb: building package 'libgkarrays1' in '../libgkarrays1_2.1.0+dfsg-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libgkarrays_2.1.0+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../libgkarrays_2.1.0+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1121,12 +1162,14 @@ 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/11956/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/11956/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/2778 and its subdirectories -I: Current time: Thu May 30 08:54:17 -12 2024 -I: pbuilder-time-stamp: 1717102457 +I: removing directory /srv/workspace/pbuilder/11956 and its subdirectories +I: Current time: Sat Apr 29 04:33:00 +14 2023 +I: pbuilder-time-stamp: 1682692380