Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 11:59:22.995637461 +0000 +++ b2/build.log 2024-05-07 12:06:17.026016594 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 23:52:14 -12 2024 -I: pbuilder-time-stamp: 1715082734 +I: Current time: Tue Jun 10 08:22:26 +14 2025 +I: pbuilder-time-stamp: 1749493346 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,51 +29,83 @@ dpkg-source: info: applying fix-privacy-breach.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1207255/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2285218/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 9 18:22 /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/2285218/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2285218/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='172d13e02f4e4b45ba80504ac18c649a' - 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='1207255' - PS1='# ' - PS2='> ' + INVOCATION_ID=c470ec0b21c34eeeb0473f6fee039571 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2285218 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.bstw1hvP/pbuilderrc_xefe --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.bstw1hvP/b1 --logfile b1/build.log abyss_2.3.7-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.bstw1hvP/pbuilderrc_cXkz --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.bstw1hvP/b2 --logfile b2/build.log abyss_2.3.7-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 6 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1207255/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 8 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2285218/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -272,7 +304,7 @@ Get: 143 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 135 MB in 1s (115 MB/s) +Fetched 135 MB in 1s (106 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19699 files and directories currently installed.) @@ -871,7 +903,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/abyss-2.3.7/ && 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 > ../abyss_2.3.7-3_source.changes +I: user script /srv/workspace/pbuilder/2285218/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2285218/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/abyss-2.3.7/ && 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 > ../abyss_2.3.7-3_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.7-3 dpkg-buildpackage: info: source distribution unstable @@ -916,8 +952,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk @@ -1152,19 +1188,19 @@ ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataLayer' Making all in DataBase make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' Making all in FMIndex make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/FMIndex' @@ -1198,6 +1234,23 @@ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o translate.o translate.c +io.c: In function 'read_scr_matrix': +io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 270 | fscanf( fp, "%i", &is); + | ^~~~~~~~~~~~~~~~~~~~~~ +io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fscanf(fp, "%s\n", rline); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +io.c: In function 'read_diag_prob_dist': +io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined + 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, + | ^~~~~~~~~~~~~~ +alig.c:13:20: warning: inline function 'calc_weight' declared but never defined + 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + | ^~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ @@ -1213,23 +1266,6 @@ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ -alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined - 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, - | ^~~~~~~~~~~~~~ -alig.c:13:20: warning: inline function 'calc_weight' declared but never defined - 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, - | ^~~~~~~~~~~ -io.c: In function 'read_scr_matrix': -io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 270 | fscanf( fp, "%i", &is); - | ^~~~~~~~~~~~~~~~~~~~~~ -io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 282 | fscanf(fp, "%s\n", rline); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -io.c: In function 'read_diag_prob_dist': -io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diag.c:1456:17: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ @@ -1251,8 +1287,8 @@ ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Align' Making all in ABYSS make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/ABYSS' @@ -1271,8 +1307,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Parallel' Making all in Bloom make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Bloom' @@ -1306,8 +1342,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/KAligner' @@ -1359,8 +1395,8 @@ | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Map' Making all in MergePaths make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/MergePaths' @@ -1453,8 +1489,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/PathOverlap' @@ -1523,8 +1559,8 @@ ../Graph/DotIO.h:44:51: note: the temporary was destroyed at the end of the full expression 'get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))' 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ -g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Scaffold' Making all in SimpleGraph @@ -1806,14 +1842,14 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.7 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.7/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc -rm -f libgtest_main.a -ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o -ar: `u' modifier ignored since `D' is the default (see `U') -ranlib libgtest_main.a rm -f libgtest.a ar cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a +rm -f libgtest_main.a +ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o +ar: `u' modifier ignored since `D' is the default (see `U') +ranlib libgtest_main.a make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7/vendor/gtest-1.7.0' Making check in Unittest @@ -1869,7 +1905,6 @@ g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm @@ -1881,51 +1916,52 @@ g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Unittest' make check-TESTS make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Unittest' PASS: common_histogram +PASS: common_kmer +PASS: common_sequence PASS: common_bitutil PASS: common_stringutil PASS: common_KmerIterator -PASS: common_sequence -PASS: common_kmer -PASS: common_sam -PASS: BloomFilter -PASS: graph_AllPathsSearch -PASS: graph_HashGraph -PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: Konnector_DBGBloom PASS: common_sam_ssq +PASS: BloomFilter +PASS: common_sam +PASS: Konnector_DBGBloomAlgorithms +PASS: graph_AllPathsSearch +PASS: graph_HashGraph PASS: graph_BidirectionalBFS -PASS: graph_DotIO +PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_UndirectedGraph -PASS: graph_ConstrainedBidiBFSVisitor +PASS: graph_DotIO PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc -PASS: BloomDBG_BloomDBG PASS: PairedDBG_BranchRecord -PASS: BloomDBG_HashAgnosticCascadingBloom -PASS: BloomDBG_RollingHashIterator -PASS: BloomDBG_CountingBloomFilter +PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash +PASS: BloomDBG_CountingBloomFilter +PASS: BloomDBG_RollingHashIterator +PASS: BloomDBG_RollingBloomDBG +PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer -PASS: BloomDBG_RollingBloomDBG -PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm +PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.3.7 ============================================================================ @@ -1992,11 +2028,11 @@ Making install in DataBase make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/DataBase' - /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' - /usr/bin/install -c abyss-db-txt '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' + /usr/bin/install -c abyss-db-txt '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/DataBase' Making install in FMIndex @@ -2135,8 +2171,8 @@ Making install in Overlap make[3]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[4]: Entering directory '/build/reproducible-path/abyss-2.3.7/Overlap' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Overlap '/build/reproducible-path/abyss-2.3.7/debian/tmp/usr/bin' make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7/Overlap' @@ -2264,10 +2300,10 @@ make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.7' make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.7' mkdir -p debian/tmp/usr/share/man/man1 -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 -PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ +PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.7' @@ -2295,8 +2331,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.7-3_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.7-3_amd64.deb'. +dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.7-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.7-3_amd64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.7-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2304,12 +2340,14 @@ 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/2285218/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2285218/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/1207255 and its subdirectories -I: Current time: Mon May 6 23:59:21 -12 2024 -I: pbuilder-time-stamp: 1715083161 +I: removing directory /srv/workspace/pbuilder/2285218 and its subdirectories +I: Current time: Tue Jun 10 08:29:15 +14 2025 +I: pbuilder-time-stamp: 1749493755