Diff of the two buildlogs: -- --- b1/build.log 2024-05-11 10:45:10.839550525 +0000 +++ b2/build.log 2024-05-11 10:51:00.304679581 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 10 22:15:35 -12 2024 -I: pbuilder-time-stamp: 1715422536 +I: Current time: Sat Jun 14 07:08:14 +14 2025 +I: pbuilder-time-stamp: 1749834494 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying create_doc_without_previous_binary_build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2525188/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4167960/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 13 17:08 /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/4167960/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4167960/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8381411e1fa240cf8731f736afdbdcbd' - 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='2525188' - PS1='# ' - PS2='> ' + INVOCATION_ID=7be590149fc94e5d831267ce4466a229 + 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=4167960 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.QBF952Fg/pbuilderrc_ralY --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QBF952Fg/b1 --logfile b1/build.log seqan-needle_1.0.2+ds-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.QBF952Fg/pbuilderrc_gIDb --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QBF952Fg/b2 --logfile b2/build.log seqan-needle_1.0.2+ds-2.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-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 10 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2525188/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 11 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4167960/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -197,7 +229,7 @@ Get: 71 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 92.4 MB in 4s (26.1 MB/s) +Fetched 92.4 MB in 2s (60.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (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.) @@ -504,7 +536,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/seqan-needle-1.0.2+ds/ && 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 > ../seqan-needle_1.0.2+ds-2_source.changes +I: user script /srv/workspace/pbuilder/4167960/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4167960/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/seqan-needle-1.0.2+ds/ && 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 > ../seqan-needle_1.0.2+ds-2_source.changes dpkg-buildpackage: info: source package seqan-needle dpkg-buildpackage: info: source version 1.0.2+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -542,8 +578,8 @@ -- Found Doxygen: /usr/bin/doxygen -- You can run `make doc` to build api documentation. -- You can run `make test` to build and run tests. --- Configuring done (30.5s) --- Generating done (0.1s) +-- Configuring done (5.1s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -562,7 +598,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/seqan-needle-1.0.2+ds' dh_auto_build --arch - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/seqan-needle-1.0.2+ds -B/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -575,8 +611,8 @@ make -f src/CMakeFiles/needle_lib.dir/build.make src/CMakeFiles/needle_lib.dir/build make[4]: Entering directory '/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/needle_lib.dir/ibf.cpp.o -cd /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/build/reproducible-path/seqan-needle-1.0.2+ds/src/../include -I/build/reproducible-path/seqan-needle-1.0.2+ds/lib/robin-hood-hashing/src/include -isystem /usr/include/seqan3/submodules/sdsl-lite/include -g -O2 -ffile-prefix-map=/build/reproducible-path/seqan-needle-1.0.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -fopenmp -MD -MT src/CMakeFiles/needle_lib.dir/ibf.cpp.o -MF CMakeFiles/needle_lib.dir/ibf.cpp.o.d -o CMakeFiles/needle_lib.dir/ibf.cpp.o -c /build/reproducible-path/seqan-needle-1.0.2+ds/src/ibf.cpp [ 40%] Building CXX object src/CMakeFiles/needle_lib.dir/estimate.cpp.o +cd /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/build/reproducible-path/seqan-needle-1.0.2+ds/src/../include -I/build/reproducible-path/seqan-needle-1.0.2+ds/lib/robin-hood-hashing/src/include -isystem /usr/include/seqan3/submodules/sdsl-lite/include -g -O2 -ffile-prefix-map=/build/reproducible-path/seqan-needle-1.0.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -fopenmp -MD -MT src/CMakeFiles/needle_lib.dir/ibf.cpp.o -MF CMakeFiles/needle_lib.dir/ibf.cpp.o.d -o CMakeFiles/needle_lib.dir/ibf.cpp.o -c /build/reproducible-path/seqan-needle-1.0.2+ds/src/ibf.cpp cd /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN3_HAS_BZIP2=1 -DSEQAN3_HAS_ZLIB=1 -I/build/reproducible-path/seqan-needle-1.0.2+ds/src/../include -I/build/reproducible-path/seqan-needle-1.0.2+ds/lib/robin-hood-hashing/src/include -isystem /usr/include/seqan3/submodules/sdsl-lite/include -g -O2 -ffile-prefix-map=/build/reproducible-path/seqan-needle-1.0.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++20 -fopenmp -MD -MT src/CMakeFiles/needle_lib.dir/estimate.cpp.o -MF CMakeFiles/needle_lib.dir/estimate.cpp.o.d -o CMakeFiles/needle_lib.dir/estimate.cpp.o -c /build/reproducible-path/seqan-needle-1.0.2+ds/src/estimate.cpp /build/reproducible-path/seqan-needle-1.0.2+ds/src/ibf.cpp: In function ‘void fill_hash_table_parallel(const min_arguments&, seqan3::sequence_file_input >&, robin_hood::unordered_node_map&, robin_hood::unordered_node_map&, robin_hood::unordered_set&, robin_hood::unordered_set&, bool, uint8_t)’: /build/reproducible-path/seqan-needle-1.0.2+ds/src/ibf.cpp:242:38: warning: narrowing conversion of ‘thread_count’ from ‘size_t’ {aka ‘long unsigned int’} to ‘ptrdiff_t’ {aka ‘long int’} [-Wnarrowing] @@ -775,10 +811,10 @@ Do Nothing make[1]: Leaving directory '/build/reproducible-path/seqan-needle-1.0.2+ds' dh_auto_test -Nseqan-needle-doc - cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[1]: Entering directory '/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j20 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu @@ -1356,41 +1392,64 @@ 1: [----------] Global test environment set-up. 1: [----------] 3 tests from count 1: [ RUN ] count.small_example -1: [ OK ] count.small_example (9 ms) +1: [ OK ] count.small_example (1 ms) 1: [ RUN ] count.small_example_paired -1: [ OK ] count.small_example_paired (4 ms) +1: [ OK ] count.small_example_paired (1 ms) 1: [ RUN ] count.small_example_exclude -1: [ OK ] count.small_example_exclude (2 ms) -1: [----------] 3 tests from count (16 ms total) +1: [ OK ] count.small_example_exclude (0 ms) +1: [----------] 3 tests from count (2 ms total) 1: 1: [----------] 1 test from genome 1: [ RUN ] genome.small_example -1: [ OK ] genome.small_example (2 ms) -1: [----------] 1 test from genome (2 ms total) +1: [ OK ] genome.small_example (0 ms) +1: [----------] 1 test from genome (0 ms total) 1: 1: [----------] Global test environment tear-down -1: [==========] 4 tests from 2 test suites ran. (18 ms total) +1: [==========] 4 tests from 2 test suites ran. (3 ms total) 1: [ PASSED ] 4 tests. 2: Running main() from ./googletest/src/gtest_main.cc 2: [==========] Running 9 tests from 2 test suites. 2: [----------] Global test environment set-up. 2: [----------] 1 test from delete 2: [ RUN ] delete.no_given_thresholds +2: [ OK ] delete.no_given_thresholds (3 ms) +2: [----------] 1 test from delete (3 ms total) +2: +2: [----------] 8 tests from insert +2: [ RUN ] insert.ibf +2: [ OK ] insert.ibf (2 ms) +2: [ RUN ] insert.ibf_no_given_thresholds +2: [ OK ] insert.ibf_no_given_thresholds (1 ms) +2: [ RUN ] insert.ibf_delete +2: [ OK ] insert.ibf_delete (4 ms) +2: [ RUN ] insert.ibf_delete_no_given_threshold +2: [ OK ] insert.ibf_delete_no_given_threshold (2 ms) +2: [ RUN ] insert.ibfmin 3: Running main() from ./googletest/src/gtest_main.cc 3: [==========] Running 10 tests from 1 test suite. 3: [----------] Global test environment set-up. 3: [----------] 10 tests from estimate 3: [ RUN ] estimate.small_example -3: [ OK ] estimate.small_example (7 ms) +3: [ OK ] estimate.small_example (2 ms) 3: [ RUN ] estimate.small_example_uncompressed +3: [ OK ] estimate.small_example_uncompressed (1 ms) +3: [ RUN ] estimate.small_example_gene_not_found +3: [ OK ] estimate.small_example_gene_not_found (0 ms) +3: [ RUN ] estimate.small_example_different_expressions_per_level +3: [ OK ] estimate.small_example_different_expressions_per_level (1 ms) +3: [ RUN ] estimate.small_example_different_expressions_per_level_normalization_1 +3: [ OK ] estimate.small_example_different_expressions_per_level_normalization_1 (0 ms) +3: [ RUN ] estimate.small_example_different_expressions_per_level_normalization_1_uncompressed +3: [ OK ] estimate.small_example_different_expressions_per_level_normalization_1_uncompressed (0 ms) +3: [ RUN ] estimate.example 4: Running main() from ./googletest/src/gtest_main.cc 4: [==========] Running 8 tests from 1 test suite. 4: [----------] Global test environment set-up. 4: [----------] 8 tests from ibf 4: [ RUN ] ibf.given_expression_thresholds -4: [ OK ] ibf.given_expression_thresholds (7 ms) +4: [ OK ] ibf.given_expression_thresholds (1 ms) 4: [ RUN ] ibf.given_expression_thresholds_include_file -4: [ OK ] ibf.given_expression_thresholds_include_file (1 ms) +4: [ OK ] ibf.given_expression_thresholds_include_file (0 ms) 4: [ RUN ] ibf.given_expression_thresholds_exclude_file 4: [ OK ] ibf.given_expression_thresholds_exclude_file (0 ms) 4: [ RUN ] ibf.no_given_expression_thresholds @@ -1398,9 +1457,9 @@ 4: [ RUN ] ibf.expression_thresholds_by_genome 4: [ OK ] ibf.expression_thresholds_by_genome (0 ms) 4: [ RUN ] ibf.throws -4: [ OK ] ibf.throws (7 ms) +4: [ OK ] ibf.throws (0 ms) 4: [ RUN ] ibf.given_cutoffs -4: [ OK ] ibf.given_cutoffs (1 ms) +4: [ OK ] ibf.given_cutoffs (0 ms) 4: [ RUN ] ibf.different_file_sizes 5: Running main() from ./googletest/src/gtest_main.cc 5: [==========] Running 4 tests from 1 test suite. @@ -1411,65 +1470,73 @@ 5: [ RUN ] ibfmin.no_given_expression_thresholds 5: [ OK ] ibfmin.no_given_expression_thresholds (0 ms) 5: [ RUN ] ibfmin.expression_thresholds_by_genome -5: [ OK ] ibfmin.expression_thresholds_by_genome (2 ms) +5: [ OK ] ibfmin.expression_thresholds_by_genome (1 ms) 5: [ RUN ] ibfmin.different_shape -5: [ OK ] ibfmin.different_shape (1 ms) -5: [----------] 4 tests from ibfmin (5 ms total) +5: [ OK ] ibfmin.different_shape (0 ms) +5: [----------] 4 tests from ibfmin (2 ms total) 5: 5: [----------] Global test environment tear-down -5: [==========] 4 tests from 1 test suite ran. (5 ms total) +5: [==========] 4 tests from 1 test suite ran. (3 ms total) 5: [ PASSED ] 4 tests. 6: Running main() from ./googletest/src/gtest_main.cc 6: [==========] Running 8 tests from 1 test suite. 6: [----------] Global test environment set-up. 6: [----------] 8 tests from minimiser 6: [ RUN ] minimiser.small_example -6: [ OK ] minimiser.small_example (16 ms) +6: [ OK ] minimiser.small_example (2 ms) 6: [ RUN ] minimiser.small_example_different_shape -6: [ OK ] minimiser.small_example_different_shape (1 ms) +6: [ OK ] minimiser.small_example_different_shape (0 ms) 6: [ RUN ] minimiser.small_example_samplewise 6: [ OK ] minimiser.small_example_samplewise (0 ms) 6: [ RUN ] minimiser.cutoff_by_filesize 6: [ OK ] minimiser.cutoff_by_filesize (0 ms) 6: [ RUN ] minimiser.small_example_two_threads -6: [ OK ] minimiser.small_example_two_threads (2 ms) +6: [ OK ] minimiser.small_example_two_threads (1 ms) 6: [ RUN ] minimiser.small_example_include 6: [ OK ] minimiser.small_example_include (0 ms) 6: [ RUN ] minimiser.small_example_exclude 6: [ OK ] minimiser.small_example_exclude (0 ms) 6: [ RUN ] minimiser.small_example_shape -6: [ OK ] minimiser.small_example_shape (1 ms) -6: [----------] 8 tests from minimiser (25 ms total) +6: [ OK ] minimiser.small_example_shape (0 ms) +6: [----------] 8 tests from minimiser (6 ms total) 6: 6: [----------] Global test environment tear-down -6: [==========] 8 tests from 1 test suite ran. (25 ms total) +6: [==========] 8 tests from 1 test suite ran. (6 ms total) 6: [ PASSED ] 8 tests. 7: Running main() from ./googletest/src/gtest_main.cc 7: [==========] Running 2 tests from 1 test suite. 7: [----------] Global test environment set-up. 7: [----------] 2 tests from needle_options_test 7: [ RUN ] needle_options_test.no_options -7: [ OK ] needle_options_test.no_options (64 ms) +7: [ OK ] needle_options_test.no_options (4 ms) 7: [ RUN ] needle_options_test.fail_no_argument +7: [ OK ] needle_options_test.fail_no_argument (4 ms) +7: [----------] 2 tests from needle_options_test (8 ms total) +7: +7: [----------] Global test environment tear-down +7: [==========] 2 tests from 1 test suite ran. (8 ms total) +7: [ PASSED ] 2 tests. 8: Running main() from ./googletest/src/gtest_main.cc 8: [==========] Running 19 tests from 1 test suite. 8: [----------] Global test environment set-up. 8: [----------] 19 tests from ibf_options_test 8: [ RUN ] ibf_options_test.ibf_no_options -8: [ OK ] ibf_options_test.ibf_no_options (56 ms) +8: [ OK ] ibf_options_test.ibf_no_options (4 ms) 8: [ RUN ] ibf_options_test.ibf_fail_no_argument 9: Running main() from ./googletest/src/gtest_main.cc 9: [==========] Running 3 tests from 1 test suite. 9: [----------] Global test environment set-up. 9: [----------] 3 tests from insert_options_test 9: [ RUN ] insert_options_test.insert_no_options -9: [ OK ] insert_options_test.insert_no_options (46 ms) +9: [ OK ] insert_options_test.insert_no_options (4 ms) 9: [ RUN ] insert_options_test.insert_fail_no_argument 10: Running main() from ./googletest/src/gtest_main.cc 10: [==========] Running 8 tests from 1 test suite. 10: [----------] Global test environment set-up. 10: [----------] 8 tests from minimiser_options_test 10: [ RUN ] minimiser_options_test.no_options +10: [ OK ] minimiser_options_test.no_options (4 ms) +10: [ RUN ] minimiser_options_test.fail_no_argument 11: Running main() from ./googletest/src/gtest_main.cc 11: [==========] Running 5 tests from 1 test suite. 11: [----------] Global test environment set-up. @@ -1480,200 +1547,169 @@ 12: [----------] Global test environment set-up. 12: [----------] 5 tests from count_options_test 12: [ RUN ] count_options_test.no_options - 1/13 Test #1: test/api/count_test ............... Passed 0.17 sec - 2/13 Test #5: test/api/ibfmin_test .............. Passed 0.11 sec - 3/13 Test #6: test/api/minimiser_test ........... Passed 0.11 sec -10: [ OK ] minimiser_options_test.no_options (28 ms) -10: [ RUN ] minimiser_options_test.fail_no_argument + 1/13 Test #1: test/api/count_test ............... Passed 0.02 sec + 2/13 Test #5: test/api/ibfmin_test .............. Passed 0.02 sec + 3/13 Test #6: test/api/minimiser_test ........... Passed 0.01 sec +2: [ OK ] insert.ibfmin (1 ms) +2: [ RUN ] insert.ibfmin_delete + 4/13 Test #7: test/cli/needle_options_test ...... Passed 0.01 sec 13: Running main() from ./googletest/src/gtest_main.cc 13: [==========] Running 2 tests from 1 test suite. 13: [----------] Global test environment set-up. 13: [----------] 2 tests from delete_options_test 13: [ RUN ] delete_options_test.delete_no_options -11: [ OK ] estimate_options_test.no_options (35 ms) +11: [ OK ] estimate_options_test.no_options (4 ms) 11: [ RUN ] estimate_options_test.fail_no_argument -7: [ OK ] needle_options_test.fail_no_argument (28 ms) -7: [----------] 2 tests from needle_options_test (92 ms total) -7: -7: [----------] Global test environment tear-down -7: [==========] 2 tests from 1 test suite ran. (93 ms total) -7: [ PASSED ] 2 tests. - 4/13 Test #7: test/cli/needle_options_test ...... Passed 0.10 sec -13: [ OK ] delete_options_test.delete_no_options (18 ms) -13: [ RUN ] delete_options_test.with_argument -8: [ OK ] ibf_options_test.ibf_fail_no_argument (35 ms) +8: [ OK ] ibf_options_test.ibf_fail_no_argument (4 ms) 8: [ RUN ] ibf_options_test.ibf_fail_contradiction -12: [ OK ] count_options_test.no_options (41 ms) -12: [ RUN ] count_options_test.fail_no_argument -9: [ OK ] insert_options_test.insert_fail_no_argument (36 ms) +2: [ OK ] insert.ibfmin_delete (2 ms) +2: [ RUN ] insert.ibfmin_no_given_thresholds +9: [ OK ] insert_options_test.insert_fail_no_argument (4 ms) 9: [ RUN ] insert_options_test.with_argument -2: [ OK ] delete.no_given_thresholds (143 ms) -2: [----------] 1 test from delete (143 ms total) -2: -2: [----------] 8 tests from insert -2: [ RUN ] insert.ibf -10: [ OK ] minimiser_options_test.fail_no_argument (35 ms) +12: [ OK ] count_options_test.no_options (4 ms) +12: [ RUN ] count_options_test.fail_no_argument +2: [ OK ] insert.ibfmin_no_given_thresholds (1 ms) +2: [ RUN ] insert.delete_ibfmin_no_given_thresholds +10: [ OK ] minimiser_options_test.fail_no_argument (4 ms) 10: [ RUN ] minimiser_options_test.with_arguments -11: [ OK ] estimate_options_test.fail_no_argument (30 ms) +13: [ OK ] delete_options_test.delete_no_options (4 ms) +13: [ RUN ] delete_options_test.with_argument +11: [ OK ] estimate_options_test.fail_no_argument (4 ms) 11: [ RUN ] estimate_options_test.with_argument -12: [ OK ] count_options_test.fail_no_argument (20 ms) -12: [ RUN ] count_options_test.with_arguments -8: [ OK ] ibf_options_test.ibf_fail_contradiction (40 ms) +8: [ OK ] ibf_options_test.ibf_fail_contradiction (4 ms) 8: [ RUN ] ibf_options_test.ibf_fail_contradiction2 -10: [ OK ] minimiser_options_test.with_arguments (47 ms) +2: [ OK ] insert.delete_ibfmin_no_given_thresholds (2 ms) +2: [----------] 8 tests from insert (19 ms total) +2: +2: [----------] Global test environment tear-down +2: [==========] 9 tests from 2 test suites ran. (22 ms total) +2: [ PASSED ] 9 tests. + 5/13 Test #2: test/api/insert_delete_test ....... Passed 0.03 sec +12: [ OK ] count_options_test.fail_no_argument (4 ms) +12: [ RUN ] count_options_test.with_arguments +10: [ OK ] minimiser_options_test.with_arguments (5 ms) 10: [ RUN ] minimiser_options_test.cutoff -12: [ OK ] count_options_test.with_arguments (55 ms) +8: [ OK ] ibf_options_test.ibf_fail_contradiction2 (5 ms) +8: [ RUN ] ibf_options_test.ibf_fail_no_fpr +12: [ OK ] count_options_test.with_arguments (7 ms) 12: [ RUN ] count_options_test.multithreads -3: [ OK ] estimate.small_example_uncompressed (192 ms) -3: [ RUN ] estimate.small_example_gene_not_found -3: [ OK ] estimate.small_example_gene_not_found (1 ms) -3: [ RUN ] estimate.small_example_different_expressions_per_level -3: [ OK ] estimate.small_example_different_expressions_per_level (5 ms) -3: [ RUN ] estimate.small_example_different_expressions_per_level_normalization_1 -10: [ OK ] minimiser_options_test.cutoff (35 ms) +8: [ OK ] ibf_options_test.ibf_fail_no_fpr (3 ms) +8: [ RUN ] ibf_options_test.ibf_fail_incorrect_number_of_fprs +10: [ OK ] minimiser_options_test.cutoff (5 ms) 10: [ RUN ] minimiser_options_test.multiple_sample -3: [ OK ] estimate.small_example_different_expressions_per_level_normalization_1 (11 ms) -3: [ RUN ] estimate.small_example_different_expressions_per_level_normalization_1_uncompressed -3: [ OK ] estimate.small_example_different_expressions_per_level_normalization_1_uncompressed (4 ms) -3: [ RUN ] estimate.example -12: [ OK ] count_options_test.multithreads (35 ms) -12: [ RUN ] count_options_test.paired -8: [ OK ] ibf_options_test.ibf_fail_contradiction2 (79 ms) -8: [ RUN ] ibf_options_test.ibf_fail_no_fpr -10: [ OK ] minimiser_options_test.multiple_sample (47 ms) +8: [ OK ] ibf_options_test.ibf_fail_incorrect_number_of_fprs (4 ms) +8: [ RUN ] ibf_options_test.ibf_with_argument +10: [ OK ] minimiser_options_test.multiple_sample (5 ms) 10: [ RUN ] minimiser_options_test.multithreads -8: [ OK ] ibf_options_test.ibf_fail_no_fpr (48 ms) -8: [ RUN ] ibf_options_test.ibf_fail_incorrect_number_of_fprs -12: [ OK ] count_options_test.paired (79 ms) -12: [----------] 5 tests from count_options_test (233 ms total) +12: [ OK ] count_options_test.multithreads (6 ms) +12: [ RUN ] count_options_test.paired +10: [ OK ] minimiser_options_test.multithreads (5 ms) +10: [ RUN ] minimiser_options_test.paired +12: [ OK ] count_options_test.paired (5 ms) +12: [----------] 5 tests from count_options_test (29 ms total) 12: 12: [----------] 3 tests from genome_options_test 12: [ RUN ] genome_options_test.no_options -8: [ OK ] ibf_options_test.ibf_fail_incorrect_number_of_fprs (47 ms) -8: [ RUN ] ibf_options_test.ibf_with_argument -10: [ OK ] minimiser_options_test.multithreads (340 ms) -10: [ RUN ] minimiser_options_test.paired -2: [ OK ] insert.ibf (485 ms) -2: [ RUN ] insert.ibf_no_given_thresholds -12: [ OK ] genome_options_test.no_options (301 ms) +10: [ OK ] minimiser_options_test.paired (5 ms) +10: [ RUN ] minimiser_options_test.invalid_argument +12: [ OK ] genome_options_test.no_options (5 ms) 12: [ RUN ] genome_options_test.fail_no_argument -12: [ OK ] genome_options_test.fail_no_argument (36 ms) +10: [ OK ] minimiser_options_test.invalid_argument (4 ms) +10: [----------] 8 tests from minimiser_options_test (41 ms total) +10: +10: [----------] Global test environment tear-down +10: [==========] 8 tests from 1 test suite ran. (41 ms total) +10: [ PASSED ] 8 tests. + 6/13 Test #10: test/cli/minimiser_options_test ... Passed 0.04 sec +12: [ OK ] genome_options_test.fail_no_argument (5 ms) 12: [ RUN ] genome_options_test.with_arguments -10: [ OK ] minimiser_options_test.paired (107 ms) -10: [ RUN ] minimiser_options_test.invalid_argument -12: [ OK ] genome_options_test.with_arguments (69 ms) -12: [----------] 3 tests from genome_options_test (408 ms total) +12: [ OK ] genome_options_test.with_arguments (5 ms) +12: [----------] 3 tests from genome_options_test (16 ms total) 12: 12: [----------] Global test environment tear-down -12: [==========] 8 tests from 2 test suites ran. (641 ms total) +12: [==========] 8 tests from 2 test suites ran. (45 ms total) 12: [ PASSED ] 8 tests. - 5/13 Test #12: test/cli/count_options_test ....... Passed 0.65 sec -10: [ OK ] minimiser_options_test.invalid_argument (105 ms) -10: [----------] 8 tests from minimiser_options_test (749 ms total) -10: -10: [----------] Global test environment tear-down -10: [==========] 8 tests from 1 test suite ran. (750 ms total) -10: [ PASSED ] 8 tests. - 6/13 Test #10: test/cli/minimiser_options_test ... Passed 0.78 sec -2: [ OK ] insert.ibf_no_given_thresholds (559 ms) -2: [ RUN ] insert.ibf_delete -2: [ OK ] insert.ibf_delete (1742 ms) -2: [ RUN ] insert.ibf_delete_no_given_threshold -2: [ OK ] insert.ibf_delete_no_given_threshold (1350 ms) -2: [ RUN ] insert.ibfmin -2: [ OK ] insert.ibfmin (133 ms) -2: [ RUN ] insert.ibfmin_delete -2: [ OK ] insert.ibfmin_delete (523 ms) -2: [ RUN ] insert.ibfmin_no_given_thresholds -2: [ OK ] insert.ibfmin_no_given_thresholds (113 ms) -2: [ RUN ] insert.delete_ibfmin_no_given_thresholds -2: [ OK ] insert.delete_ibfmin_no_given_thresholds (258 ms) -2: [----------] 8 tests from insert (5167 ms total) -2: -2: [----------] Global test environment tear-down -2: [==========] 9 tests from 2 test suites ran. (5311 ms total) -2: [ PASSED ] 9 tests. - 7/13 Test #2: test/api/insert_delete_test ....... Passed 5.35 sec -4: [ OK ] ibf.different_file_sizes (8722 ms) -4: [----------] 8 tests from ibf (8743 ms total) + 7/13 Test #12: test/cli/count_options_test ....... Passed 0.05 sec +4: [ OK ] ibf.different_file_sizes (1560 ms) +4: [----------] 8 tests from ibf (1564 ms total) 4: 4: [----------] Global test environment tear-down -4: [==========] 8 tests from 1 test suite ran. (8743 ms total) +4: [==========] 8 tests from 1 test suite ran. (1564 ms total) 4: [ PASSED ] 8 tests. - 8/13 Test #4: test/api/ibf_test ................. Passed 8.77 sec -3: [ OK ] estimate.example (55194 ms) + 8/13 Test #4: test/api/ibf_test ................. Passed 1.57 sec +8: [ OK ] ibf_options_test.ibf_with_argument (2499 ms) +8: [ RUN ] ibf_options_test.ibf_with_argument_with_options +3: [ OK ] estimate.example (3089 ms) 3: [ RUN ] estimate.example_multiple_threads -9: [ OK ] insert_options_test.with_argument (87891 ms) -9: [----------] 3 tests from insert_options_test (87974 ms total) +11: [ OK ] estimate_options_test.with_argument (3745 ms) +11: [ RUN ] estimate_options_test.with_argument_normalization_method +9: [ OK ] insert_options_test.with_argument (3921 ms) +9: [----------] 3 tests from insert_options_test (3929 ms total) 9: 9: [----------] Global test environment tear-down -9: [==========] 3 tests from 1 test suite ran. (87974 ms total) +9: [==========] 3 tests from 1 test suite ran. (3929 ms total) 9: [ PASSED ] 3 tests. - 9/13 Test #9: test/cli/insert_options_test ...... Passed 88.00 sec -8: [ OK ] ibf_options_test.ibf_with_argument (96136 ms) -8: [ RUN ] ibf_options_test.ibf_with_argument_with_options -3: [ OK ] estimate.example_multiple_threads (48427 ms) + 9/13 Test #9: test/cli/insert_options_test ...... Passed 3.93 sec +8: [ OK ] ibf_options_test.ibf_with_argument_with_options (2765 ms) +8: [ RUN ] ibf_options_test.ibf_with_argument_with_userdefined_shape +3: [ OK ] estimate.example_multiple_threads (3097 ms) 3: [ RUN ] estimate.example_different_expressions_per_level -11: [ OK ] estimate_options_test.with_argument (105054 ms) -11: [ RUN ] estimate_options_test.with_argument_normalization_method -3: [ OK ] estimate.example_different_expressions_per_level (2136 ms) +3: [ OK ] estimate.example_different_expressions_per_level (1119 ms) 3: [ RUN ] estimate.example_different_expressions_per_level_multiple_threads -3: [ OK ] estimate.example_different_expressions_per_level_multiple_threads (3394 ms) -3: [----------] 10 tests from estimate (109384 ms total) -3: -3: [----------] Global test environment tear-down -3: [==========] 10 tests from 1 test suite ran. (109384 ms total) -3: [ PASSED ] 10 tests. -10/13 Test #3: test/api/estimate_test ............ Passed 109.45 sec -8: [ OK ] ibf_options_test.ibf_with_argument_with_options (90172 ms) -8: [ RUN ] ibf_options_test.ibf_with_argument_with_userdefined_shape -13: [ OK ] delete_options_test.with_argument (256950 ms) -13: [----------] 2 tests from delete_options_test (256973 ms total) +13: [ OK ] delete_options_test.with_argument (7587 ms) +13: [----------] 2 tests from delete_options_test (7591 ms total) 13: 13: [----------] Global test environment tear-down -13: [==========] 2 tests from 1 test suite ran. (256973 ms total) +13: [==========] 2 tests from 1 test suite ran. (7591 ms total) 13: [ PASSED ] 2 tests. -11/13 Test #13: test/cli/delete_options_test ...... Passed 257.00 sec -11: [ OK ] estimate_options_test.with_argument_normalization_method (154642 ms) +10/13 Test #13: test/cli/delete_options_test ...... Passed 7.60 sec +3: [ OK ] estimate.example_different_expressions_per_level_multiple_threads (1544 ms) +3: [----------] 10 tests from estimate (8857 ms total) +3: +3: [----------] Global test environment tear-down +3: [==========] 10 tests from 1 test suite ran. (8857 ms total) +3: [ PASSED ] 10 tests. +11/13 Test #3: test/api/estimate_test ............ Passed 8.86 sec +11: [ OK ] estimate_options_test.with_argument_normalization_method (19585 ms) 11: [ RUN ] estimate_options_test.with_argument_out -8: [ OK ] ibf_options_test.ibf_with_argument_with_userdefined_shape (100835 ms) +8: [ OK ] ibf_options_test.ibf_with_argument_with_userdefined_shape (26554 ms) 8: [ RUN ] ibf_options_test.ibfmin_no_options -8: [ OK ] ibf_options_test.ibfmin_no_options (20 ms) +8: [ OK ] ibf_options_test.ibfmin_no_options (4 ms) 8: [ RUN ] ibf_options_test.ibfmin_fail_no_argument -8: [ OK ] ibf_options_test.ibfmin_fail_no_argument (174 ms) +8: [ OK ] ibf_options_test.ibfmin_fail_no_argument (4 ms) 8: [ RUN ] ibf_options_test.ibfmin_fail_contradiction -8: [ OK ] ibf_options_test.ibfmin_fail_contradiction (33 ms) +8: [ OK ] ibf_options_test.ibfmin_fail_contradiction (3 ms) 8: [ RUN ] ibf_options_test.ibfmin_fail_contradiction2 -8: [ OK ] ibf_options_test.ibfmin_fail_contradiction2 (115 ms) +8: [ OK ] ibf_options_test.ibfmin_fail_contradiction2 (4 ms) 8: [ RUN ] ibf_options_test.ibfmin_fail_no_fpr -8: [ OK ] ibf_options_test.ibfmin_fail_no_fpr (21 ms) +8: [ OK ] ibf_options_test.ibfmin_fail_no_fpr (4 ms) 8: [ RUN ] ibf_options_test.ibfmin_fail_incorrect_number_of_fprs -8: [ OK ] ibf_options_test.ibfmin_fail_incorrect_number_of_fprs (26 ms) +8: [ OK ] ibf_options_test.ibfmin_fail_incorrect_number_of_fprs (3 ms) 8: [ RUN ] ibf_options_test.ibfmin_with_argument -8: [ OK ] ibf_options_test.ibfmin_with_argument (33 ms) +8: [ OK ] ibf_options_test.ibfmin_with_argument (4 ms) 8: [ RUN ] ibf_options_test.compressed -8: [ OK ] ibf_options_test.compressed (130 ms) +8: [ OK ] ibf_options_test.compressed (4 ms) 8: [ RUN ] ibf_options_test.more_hash_functions -8: [ OK ] ibf_options_test.more_hash_functions (228 ms) +8: [ OK ] ibf_options_test.more_hash_functions (4 ms) 8: [ RUN ] ibf_options_test.expression_thresholds -8: [ OK ] ibf_options_test.expression_thresholds (31 ms) -8: [----------] 19 tests from ibf_options_test (288268 ms total) +8: [ OK ] ibf_options_test.expression_thresholds (3 ms) +8: [----------] 19 tests from ibf_options_test (31887 ms total) 8: 8: [----------] Global test environment tear-down -8: [==========] 19 tests from 1 test suite ran. (288276 ms total) +8: [==========] 19 tests from 1 test suite ran. (31887 ms total) 8: [ PASSED ] 19 tests. -12/13 Test #8: test/cli/ibf_options_test ......... Passed 288.35 sec -11: [ OK ] estimate_options_test.with_argument_out (42915 ms) -11: [----------] 5 tests from estimate_options_test (302679 ms total) +12/13 Test #8: test/cli/ibf_options_test ......... Passed 31.89 sec +11: [ OK ] estimate_options_test.with_argument_out (22082 ms) +11: [----------] 5 tests from estimate_options_test (45423 ms total) 11: 11: [----------] Global test environment tear-down -11: [==========] 5 tests from 1 test suite ran. (302690 ms total) +11: [==========] 5 tests from 1 test suite ran. (45423 ms total) 11: [ PASSED ] 5 tests. -13/13 Test #11: test/cli/estimate_options_test .... Passed 302.73 sec +13/13 Test #11: test/cli/estimate_options_test .... Passed 45.43 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 1083.17 sec +Total Test time (real) = 210.03 sec make[1]: Leaving directory '/build/reproducible-path/seqan-needle-1.0.2+ds/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep @@ -1696,9 +1732,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'seqan-needle-doc' in '../seqan-needle-doc_1.0.2+ds-2_all.deb'. dpkg-deb: building package 'seqan-needle' in '../seqan-needle_1.0.2+ds-2_amd64.deb'. dpkg-deb: building package 'seqan-needle-dbgsym' in '../seqan-needle-dbgsym_1.0.2+ds-2_amd64.deb'. +dpkg-deb: building package 'seqan-needle-doc' in '../seqan-needle-doc_1.0.2+ds-2_all.deb'. dpkg-genbuildinfo --build=binary -O../seqan-needle_1.0.2+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../seqan-needle_1.0.2+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1706,12 +1742,14 @@ 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/4167960/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4167960/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/2525188 and its subdirectories -I: Current time: Fri May 10 22:45:09 -12 2024 -I: pbuilder-time-stamp: 1715424309 +I: removing directory /srv/workspace/pbuilder/4167960 and its subdirectories +I: Current time: Sat Jun 14 07:13:59 +14 2025 +I: pbuilder-time-stamp: 1749834839