Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 22:38:54.725041144 +0000 +++ b2/build.log 2023-06-06 23:00:21.040756976 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 8 16:38:49 -12 2024 -I: pbuilder-time-stamp: 1720499929 +I: Current time: Wed Jun 7 12:38:57 +14 2023 +I: pbuilder-time-stamp: 1686091137 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 [./abyss_2.3.5+dfsg.orig.tar.xz] I: copying [./abyss_2.3.5+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri Oct 21 23:36:18 2022 -12 +gpgv: Signature made Sun Oct 23 01:36:18 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -29,52 +29,84 @@ 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/4169/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30804/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 Jun 7 12:39 /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/30804/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30804/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='4169' - 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=30804 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.5VMHSiN9/pbuilderrc_8goS --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.5VMHSiN9/b1 --logfile b1/build.log abyss_2.3.5+dfsg-2.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.5VMHSiN9/pbuilderrc_ctH6 --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.5VMHSiN9/b2 --logfile b2/build.log --extrapackages usrmerge abyss_2.3.5+dfsg-2.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 codethink11-arm64 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jul 6 13:14 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4169/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 6 00:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/30804/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -232,7 +264,7 @@ Get: 104 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] -Fetched 66.6 MB in 4s (17.8 MB/s) +Fetched 66.6 MB in 1s (56.6 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 ... 19611 files and directories currently installed.) @@ -673,8 +705,17 @@ 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/abyss-2.3.5+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 > ../abyss_2.3.5+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/30804/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/30804/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/abyss-2.3.5+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 > ../abyss_2.3.5+dfsg-2_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -719,8 +760,8 @@ 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 @@ -983,9 +1024,6 @@ 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, | ^~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~ 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); @@ -993,6 +1031,9 @@ io.c:282:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~ 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 ); @@ -1071,8 +1112,8 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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 make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' @@ -1131,9 +1172,9 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/aarch64-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 make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' @@ -1375,21 +1416,20 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' -g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp @@ -1409,6 +1449,7 @@ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp +g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/aarch64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc @@ -1463,36 +1504,36 @@ make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' PASS: common_stringutil PASS: common_histogram -PASS: common_kmer PASS: common_bitutil +PASS: common_kmer PASS: common_KmerIterator PASS: common_sequence -PASS: BloomFilter PASS: common_sam +PASS: BloomFilter PASS: Konnector_DBGBloom -PASS: Konnector_DBGBloomAlgorithms PASS: common_sam_ssq +PASS: Konnector_DBGBloomAlgorithms +PASS: graph_ConstrainedBFSVisitor +PASS: graph_AllPathsSearch PASS: graph_BidirectionalBFS PASS: graph_HashGraph -PASS: graph_ConstrainedBFSVisitor PASS: graph_ConstrainedBidiBFSVisitor -PASS: graph_DotIO PASS: graph_ExtendPath -PASS: graph_AllPathsSearch +PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc -PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG -PASS: BloomDBG_RollingHashIterator +PASS: PairedDBG_BranchRecord PASS: BloomDBG_RollingHash -PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter +PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer -PASS: BloomDBG_LightweightKmer +PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_SpacedSeed +PASS: BloomDBG_LightweightKmer PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ @@ -1545,8 +1586,8 @@ Making install in Graph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' @@ -1561,11 +1602,11 @@ Making install in DataBase make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' - /usr/bin/install -c abyss-db-txt '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-db-csv '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' + /usr/bin/install -c abyss-db-txt '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' Making install in FMIndex @@ -1592,32 +1633,32 @@ Making install in Align make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Align' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Align' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' @@ -1632,16 +1673,16 @@ Making install in Konnector make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c konnector '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' @@ -1656,8 +1697,8 @@ Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' @@ -1672,16 +1713,16 @@ Making install in Layout make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-layout '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c logcounter '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' @@ -1696,56 +1737,56 @@ Making install in MergePaths make[3]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Overlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PathOverlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PopBubbles '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' @@ -1767,8 +1808,8 @@ Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-filtergraph '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' @@ -1790,16 +1831,16 @@ Making install in RResolver make[3]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-rresolver-short '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c AdjList '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' @@ -1833,10 +1874,10 @@ make[3]: Leaving directory '/build/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg' 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/abyss-2.3.5+dfsg' @@ -1864,8 +1905,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.5+dfsg-2_arm64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-2_arm64.deb'. +dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.5+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.5+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.5+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1873,12 +1914,14 @@ 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/30804/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30804/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/4169 and its subdirectories -I: Current time: Mon Jul 8 17:01:21 -12 2024 -I: pbuilder-time-stamp: 1720501281 +I: removing directory /srv/workspace/pbuilder/30804 and its subdirectories +I: Current time: Wed Jun 7 12:59:57 +14 2023 +I: pbuilder-time-stamp: 1686092397