Diff of the two buildlogs: -- --- b1/build.log 2024-01-11 01:20:26.722900543 +0000 +++ b2/build.log 2024-01-11 01:41:51.031449749 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 11 19:40:45 -12 2025 -I: pbuilder-time-stamp: 1739346046 +I: Current time: Thu Jan 11 15:20:32 +14 2024 +I: pbuilder-time-stamp: 1704936032 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -34,49 +34,81 @@ dpkg-source: info: applying reproducible_build I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1855804/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/529024/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Jan 11 01:21 /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/529024/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/529024/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=16 ' - DISTRIBUTION='bookworm' - 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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(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=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='62fb681e7ebf4a35a6c5e9d7eb791149' - 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='1855804' - PS1='# ' - PS2='> ' + INVOCATION_ID=0c835a36658f4bc793f3f2c284e74973 + 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=529024 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.9FqqISmo/pbuilderrc_olJr --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.9FqqISmo/b1 --logfile b1/build.log ataqv_1.3.0+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://85.184.249.68:3128' + 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.9FqqISmo/pbuilderrc_uiMj --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.9FqqISmo/b2 --logfile b2/build.log ataqv_1.3.0+ds-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -134,15 +166,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 11 01:21 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -162,7 +194,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/1855804/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/529024/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -354,7 +386,7 @@ Get: 120 http://deb.debian.org/debian bookworm/main amd64 node-d3-zoom all 1.8.3-4 [20.1 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 node-d3 all 5.16.0-10 [219 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] -Fetched 56.2 MB in 1s (87.4 MB/s) +Fetched 56.2 MB in 4s (13.3 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 ... 18148 files and directories currently installed.) @@ -859,7 +891,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ataqv-1.3.0+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 > ../ataqv_1.3.0+ds-2_source.changes +I: user script /srv/workspace/pbuilder/529024/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/529024/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ataqv-1.3.0+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 > ../ataqv_1.3.0+ds-2_source.changes dpkg-buildpackage: info: source package ataqv dpkg-buildpackage: info: source version 1.3.0+ds-2 dpkg-buildpackage: info: source distribution unstable @@ -869,7 +905,7 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean + make -j15 clean make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.0+ds' make[1]: Leaving directory '/build/reproducible-path/ataqv-1.3.0+ds' dh_clean @@ -900,7 +936,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.0+ds' dh_auto_build -- all testing/run_ataqv_tests - make -j16 "INSTALL=install --strip-program=true" all testing/run_ataqv_tests + make -j15 "INSTALL=install --strip-program=true" all testing/run_ataqv_tests make[2]: Entering directory '/build/reproducible-path/ataqv-1.3.0+ds' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o build/ataqv.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/ataqv.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o build/Features.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Features.cpp @@ -918,11 +954,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/test_utils.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_utils.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/Features.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Features.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/HTS.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/HTS.cpp -In file included from /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp:1: -/build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____172()’: -/build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp:181:44: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] - 181 | REQUIRE_THROWS_AS(rpc.add(peak3), std::out_of_range); - | ^~~~~~~~~~~~ In file included from /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_features.cpp:1: /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_features.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____167()’: /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_features.cpp:171:47: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] @@ -934,9 +965,13 @@ 200 | REQUIRE_THROWS_AS(record_to_string(header, record), HTSException); | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/IO.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/IO.cpp +In file included from /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp:1: +/build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____172()’: +/build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_peaks.cpp:181:44: warning: catching polymorphic type ‘class std::out_of_range’ by value [-Wcatch-value=] + 181 | REQUIRE_THROWS_AS(rpc.add(peak3), std::out_of_range); + | ^~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/Metrics.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Metrics.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/Peaks.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Peaks.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/Utils.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Utils.cpp In file included from /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_metrics.cpp:3: /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_metrics.cpp: In function ‘void ____C_A_T_C_H____T_E_S_T____170()’: /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_metrics.cpp:173:56: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] @@ -953,6 +988,7 @@ /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/test_metrics.cpp:259:52: warning: catching polymorphic type ‘class FileException’ by value [-Wcatch-value=] 259 | REQUIRE_THROWS_AS(collector.load_alignments(), FileException); | ^~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/Utils.o -c /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/Utils.cpp In file included from /usr/include/c++/12/bits/stl_pair.h:61, from /usr/include/c++/12/tuple:38, from /usr/include/c++/12/mutex:38, @@ -1018,6 +1054,7 @@ /build/reproducible-path/ataqv-1.3.0+ds/src/cpp/json.hpp:277:15: note: ‘’ declared here 277 | j = BasicJsonType{}; | ~~^~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/run_ataqv_tests testing/run_ataqv_tests.o testing/test_features.o testing/test_hts.o testing/test_io.o testing/test_metrics.o testing/test_peaks.o testing/test_utils.o testing/Features.o testing/HTS.o testing/IO.o testing/Metrics.o testing/Peaks.o testing/Utils.o -Wl,-z,relro -Wl,-z,now -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono -lhts -lz -lncurses -lpthread In file included from /usr/include/c++/12/bits/stl_pair.h:61, from /usr/include/c++/12/tuple:38, from /usr/include/c++/12/mutex:38, @@ -1084,11 +1121,10 @@ 277 | j = BasicJsonType{}; | ~~^~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o build/ataqv build/ataqv.o build/Features.o build/HTS.o build/IO.o build/Metrics.o build/Peaks.o build/Utils.o -Wl,-z,relro -Wl,-z,now -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono -lhts -lz -lncurses -lpthread -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/ataqv-1.3.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++11 -pthread -O3 -g -Wdate-time -D_FORTIFY_SOURCE=2 -pedantic -Wall -Wextra -Wwrite-strings -Wstrict-overflow -fno-strict-aliasing -fPIC -I/build/reproducible-path/ataqv-1.3.0+ds/src/cpp -D LINUX -o testing/run_ataqv_tests testing/run_ataqv_tests.o testing/test_features.o testing/test_hts.o testing/test_io.o testing/test_metrics.o testing/test_peaks.o testing/test_utils.o testing/Features.o testing/HTS.o testing/IO.o testing/Metrics.o testing/Peaks.o testing/Utils.o -Wl,-z,relro -Wl,-z,now -lboost_filesystem -lboost_iostreams -lboost_system -lboost_chrono -lhts -lz -lncurses -lpthread make[2]: Leaving directory '/build/reproducible-path/ataqv-1.3.0+ds' make[1]: Leaving directory '/build/reproducible-path/ataqv-1.3.0+ds' dh_auto_test - make -j16 test + make -j15 test make[1]: Entering directory '/build/reproducible-path/ataqv-1.3.0+ds' [E::sam_format1_append] Corrupted aux data for read SRR891268.122333488 Reading human autosomal references from autosomal_references.gz. @@ -1145,7 +1181,7 @@ chr20 feature count: 694 chr21 feature count: 321 chr22 feature count: 593 -Loaded 24989 TSS in 2.02776 seconds. (12323.5 TSS/second). +Loaded 24989 TSS in 6.70526 seconds. (3726.78 TSS/second). Collecting metrics from test.bam. @@ -1328,7 +1364,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 19.0562 seconds. (1956.11 peaks/second). +Loaded 37276 peaks in 34.076 seconds. (1093.91 peaks/second). Logging problematic reads to SRR891278.problems. @@ -1509,7 +1545,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 24.5989 seconds. (1515.35 peaks/second). +Loaded 37276 peaks in 93.7807 seconds. (397.48 peaks/second). New maximum proper pair fragment length: 42 from [SRR891275.608 1123 chr1 569907 57 42M = 569907 42 CACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAA @@@FFFEFFDHFBHIJIEFHJIGGF:CFGEDF?FFHEG@FGG XA:Z:chrM,+9359,42M,1; MD:Z:42 NM:i:0 AS:i:42 XS:i:37 RG:Z:SRR891275 PG:Z:MarkDuplicates] New maximum proper pair fragment length: 330 from [SRR891278.50 1123 chr1 569913 27 50M = 570193 330 NCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGC #1=DDFFFHHGHHJJJJIJJJGEGHIGGIIIJJJJIIFGGIJHIIJICHH XA:Z:chrM,+9365,50M,2; MD:Z:0C49 NM:i:1 AS:i:49 XS:i:44 RG:Z:SRR891278 PG:Z:MarkDuplicates-4FB7F45F] @@ -1547,12 +1583,12 @@ Added TSS coverage for chr2; thread count=1 Added TSS coverage for chr1; thread count=1 All TSS jobs started. Waiting for last ones to complete. -Calculated TSS coverage in 0.569982 seconds. +Calculated TSS coverage in 2.69595 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.00048434 seconds. +Calculated TSS metrics in 0.00346796 seconds. Calculating TSS metrics... -Calculated TSS metrics in 0.00053234 seconds. -Analyzed 1040 reads in 0.781898 seconds (1330.1 reads/second). +Calculated TSS metrics in 0.00309777 seconds. +Analyzed 1040 reads in 3.35069 seconds (310.384 reads/second). ataqv 1.3.0 @@ -1962,7 +1998,7 @@ chr20 peak count: 864 chr21 peak count: 487 chr22 peak count: 662 -Loaded 37276 peaks in 20.537 seconds. (1815.028 peaks/second). +Loaded 37276 peaks in 92.051 seconds. (404.949 peaks/second). New maximum proper pair fragment length: 42 from [SRR891275.608 1123 chr1 569907 57 42M = 569907 42 CACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAA @@@FFFEFFDHFBHIJIEFHJIGGF:CFGEDF?FFHEG@FGG XA:Z:chrM,+9359,42M,1; MD:Z:42 NM:i:0 AS:i:42 XS:i:37 RG:Z:SRR891275 PG:Z:MarkDuplicates] New maximum proper pair fragment length: 330 from [SRR891278.50 1123 chr1 569913 27 50M = 570193 330 NCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGC #1=DDFFFHHGHHJJJJIJJJGEGHIGGIIIJJJJIIFGGIJHIIJICHH XA:Z:chrM,+9365,50M,2; MD:Z:0C49 NM:i:1 AS:i:49 XS:i:44 RG:Z:SRR891278 PG:Z:MarkDuplicates-4FB7F45F] @@ -1971,7 +2007,7 @@ New maximum proper pair fragment length: 609 from [SRR891275.714 99 chr1 79875808 60 50M = 79876367 609 GGCCCAGCCAAGTTGACACATAAAATAAACTTTCACAATATTGCAGGCAG @@@DDDFFFHAH build/$(basename $f); install -m 0755 build/$(basename $f) /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/bin; done -install -m 0755 build/ataqv /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/bin install -d -m 0755 /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/share/ataqv/web +install -m 0755 build/ataqv /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/bin cp -a src/web/* /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/share/ataqv/web find /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/share/ataqv/web -type d -exec chmod 755 {} \; find /build/reproducible-path/ataqv-1.3.0+ds/debian/ataqv/usr/share/ataqv/web -type f -exec chmod 644 {} \; @@ -2153,8 +2189,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ataqv' in '../ataqv_1.3.0+ds-2_amd64.deb'. dpkg-deb: building package 'ataqv-dbgsym' in '../ataqv-dbgsym_1.3.0+ds-2_amd64.deb'. +dpkg-deb: building package 'ataqv' in '../ataqv_1.3.0+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ataqv_1.3.0+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../ataqv_1.3.0+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2162,12 +2198,14 @@ 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/529024/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/529024/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/1855804 and its subdirectories -I: Current time: Tue Feb 11 19:43:44 -12 2025 -I: pbuilder-time-stamp: 1739346224 +I: removing directory /srv/workspace/pbuilder/529024 and its subdirectories +I: Current time: Thu Jan 11 15:41:49 +14 2024 +I: pbuilder-time-stamp: 1704937309