Diff of the two buildlogs: -- --- b1/build.log 2019-06-26 16:37:28.668995967 +0000 +++ b2/build.log 2019-06-26 17:13:46.751595861 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 28 10:55:58 -12 2020 -I: pbuilder-time-stamp: 1595976958 +I: Current time: Thu Jun 27 06:37:32 +14 2019 +I: pbuilder-time-stamp: 1561567052 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sun Feb 17 01:20:28 2019 -12 +gpgv: Signature made Mon Feb 18 03:20:28 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-7.dsc @@ -36,6 +36,18 @@ dpkg-source: info: applying spelling I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/17948/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/17948/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -197,7 +209,7 @@ Get: 106 http://cdn-fastly.deb.debian.org/debian buster/main i386 pkg-config i386 0.29-6 [64.7 kB] Get: 107 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-pkg-resources all 40.8.0-1 [182 kB] Get: 108 http://cdn-fastly.deb.debian.org/debian buster/main i386 python-markdown all 3.0.1-3 [60.6 kB] -Fetched 49.5 MB in 3s (19.8 MB/s) +Fetched 49.5 MB in 55s (901 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -656,9 +668,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (95.6 kB/s) +Selecting previously unselected package libnumber-compare-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 ... 39340 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/abyss-2.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/abyss-2.1.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.1.5-7 dpkg-buildpackage: info: source distribution unstable @@ -687,7 +731,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -714,8 +758,8 @@ checking for ghc... no ./configure: line 5208: : command not found checking for pandoc... no -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes @@ -895,7 +939,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_build - make -j18 + make -j10 make[2]: Entering directory '/build/abyss-2.1.5' make all-recursive make[3]: Entering directory '/build/abyss-2.1.5' @@ -950,11 +994,11 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc -g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-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 ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a +g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-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/abyss-2.1.5/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.1.5/FMIndex' @@ -988,12 +1032,6 @@ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c -alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined - 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 - 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 extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ @@ -1009,9 +1047,6 @@ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ -diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static - real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); - ^~~~~~~~~~~~~~~~ io.c: In function 'read_scr_matrix': io.c:270:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%i", &is); @@ -1023,6 +1058,15 @@ io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined + 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 + extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, + ^~~~~~~~~~~ +diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static + real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); + ^~~~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1197,8 +1241,8 @@ g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm -g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm +g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-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/abyss-2.1.5/Scaffold' Making all in SimpleGraph @@ -1254,7 +1298,7 @@ markdown_py -f README.html README.md make[1]: Leaving directory '/build/abyss-2.1.5' dh_auto_test - make -j18 check VERBOSE=1 + make -j10 check VERBOSE=1 make[1]: Entering directory '/build/abyss-2.1.5' Making check in bin make[2]: Entering directory '/build/abyss-2.1.5/bin' @@ -1415,14 +1459,14 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/i386-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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') +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.a +ranlib libgtest_main.a make[3]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making check in Unittest @@ -1471,26 +1515,26 @@ g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm +g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm -g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/i386-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' @@ -1499,36 +1543,36 @@ make[4]: Entering directory '/build/abyss-2.1.5/Unittest' PASS: common_histogram PASS: common_kmer -PASS: common_bitutil -PASS: common_stringutil PASS: common_sequence +PASS: common_stringutil PASS: common_KmerIterator +PASS: common_bitutil +PASS: Konnector_DBGBloom PASS: common_sam +PASS: BloomFilter +PASS: Konnector_DBGBloomAlgorithms +PASS: graph_AllPathsSearch PASS: graph_BidirectionalBFS PASS: graph_ConstrainedBFSVisitor -PASS: graph_AllPathsSearch -PASS: Konnector_DBGBloomAlgorithms -PASS: graph_HashGraph -PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath -PASS: Konnector_DBGBloom +PASS: graph_HashGraph PASS: graph_DotIO -PASS: BloomFilter PASS: graph_UndirectedGraph +PASS: graph_ConstrainedBidiBFSVisitor PASS: Konnector_konnector PASS: PairedDBG_KmerPair -PASS: PairedDBG_BranchRecord -PASS: PairedDBG_Dinuc PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash +PASS: PairedDBG_BranchRecord PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom +PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer +PASS: PairedDBG_Dinuc PASS: BloomDBG_SpacedSeed -PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_LightweightKmer -PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm +PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.1.5 ============================================================================ @@ -1554,13 +1598,13 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_install --destdir=debian/tmp - make -j18 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no + make -j10 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.1.5' Making install in bin make[3]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/bin' make[3]: Leaving directory '/build/abyss-2.1.5/bin' @@ -1568,8 +1612,8 @@ make[3]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-2.1.5/doc' @@ -1585,7 +1629,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Graph' make[3]: Leaving directory '/build/abyss-2.1.5/Graph' @@ -1593,7 +1637,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataLayer' make[3]: Leaving directory '/build/abyss-2.1.5/DataLayer' @@ -1601,8 +1645,8 @@ make[3]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataBase' @@ -1632,7 +1676,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Align' make[3]: Leaving directory '/build/abyss-2.1.5/Align' @@ -1640,7 +1684,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ABYSS' make[3]: Leaving directory '/build/abyss-2.1.5/ABYSS' @@ -1648,7 +1692,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Parallel' make[3]: Leaving directory '/build/abyss-2.1.5/Parallel' @@ -1656,7 +1700,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Bloom' make[3]: Leaving directory '/build/abyss-2.1.5/Bloom' @@ -1664,7 +1708,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/BloomDBG' make[3]: Leaving directory '/build/abyss-2.1.5/BloomDBG' @@ -1672,7 +1716,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Konnector' make[3]: Leaving directory '/build/abyss-2.1.5/Konnector' @@ -1680,7 +1724,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Consensus' make[3]: Leaving directory '/build/abyss-2.1.5/Consensus' @@ -1688,7 +1732,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DAssembler' make[3]: Leaving directory '/build/abyss-2.1.5/DAssembler' @@ -1696,7 +1740,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DistanceEst' make[3]: Leaving directory '/build/abyss-2.1.5/DistanceEst' @@ -1704,7 +1748,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/KAligner' make[3]: Leaving directory '/build/abyss-2.1.5/KAligner' @@ -1712,7 +1756,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Layout' make[3]: Leaving directory '/build/abyss-2.1.5/Layout' @@ -1720,7 +1764,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' @@ -1728,7 +1772,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Map' make[3]: Leaving directory '/build/abyss-2.1.5/Map' @@ -1736,7 +1780,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/MergePaths' make[3]: Leaving directory '/build/abyss-2.1.5/MergePaths' @@ -1750,7 +1794,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Overlap' make[3]: Leaving directory '/build/abyss-2.1.5/Overlap' @@ -1758,7 +1802,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PairedDBG' make[3]: Leaving directory '/build/abyss-2.1.5/PairedDBG' @@ -1766,7 +1810,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns' make[3]: Leaving directory '/build/abyss-2.1.5/ParseAligns' @@ -1774,7 +1818,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PathOverlap' make[3]: Leaving directory '/build/abyss-2.1.5/PathOverlap' @@ -1782,7 +1826,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PopBubbles' make[3]: Leaving directory '/build/abyss-2.1.5/PopBubbles' @@ -1790,7 +1834,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Scaffold' make[3]: Leaving directory '/build/abyss-2.1.5/Scaffold' @@ -1798,7 +1842,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' @@ -1813,7 +1857,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/FilterGraph' make[3]: Leaving directory '/build/abyss-2.1.5/FilterGraph' @@ -1821,14 +1865,14 @@ make[3]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/GapFiller' make[3]: Leaving directory '/build/abyss-2.1.5/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-2.1.5/Sealer' make[4]: Entering directory '/build/abyss-2.1.5/Sealer' - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Sealer' make[3]: Leaving directory '/build/abyss-2.1.5/Sealer' @@ -1836,7 +1880,7 @@ make[3]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/AdjList' make[3]: Leaving directory '/build/abyss-2.1.5/AdjList' @@ -1871,15 +1915,15 @@ make[3]: Entering directory '/build/abyss-2.1.5' make[4]: Entering directory '/build/abyss-2.1.5' make[4]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' + /usr/bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.1.5' make[3]: Leaving directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' -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-2.1.5' @@ -1907,20 +1951,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_i386.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-7_i386.deb'. +dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.1.5-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/17948/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17948/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/52749 and its subdirectories -I: Current time: Tue Jul 28 11:00:27 -12 2020 -I: pbuilder-time-stamp: 1595977227 +I: removing directory /srv/workspace/pbuilder/17948 and its subdirectories +I: Current time: Thu Jun 27 07:13:45 +14 2019 +I: pbuilder-time-stamp: 1561569225