Diff of the two buildlogs: -- --- b1/build.log 2024-12-05 07:31:57.654681932 +0000 +++ b2/build.log 2024-12-05 07:35:00.686415787 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jan 7 01:54:03 -12 2026 -I: pbuilder-time-stamp: 1767794043 +I: Current time: Thu Dec 5 21:32:03 +14 2024 +I: pbuilder-time-stamp: 1733383923 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,53 +34,85 @@ dpkg-source: info: applying syntax-warning.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/18572/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21484/tmp/hooks/D01_modify_environment starting +debug: Running on infom07-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 5 07:32 /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/21484/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21484/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e8a844cf83b0407b8fa42221c6f1b353' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='18572' - PS1='# ' - PS2='> ' + INVOCATION_ID=c14cafeb1b694cc3af2853b2bda6f14e + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=21484 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.wcgTKPiN/pbuilderrc_ar8A --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wcgTKPiN/b1 --logfile b1/build.log iva_1.0.11+ds-6.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wcgTKPiN/pbuilderrc_phS7 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wcgTKPiN/b2 --logfile b2/build.log iva_1.0.11+ds-6.dsc' + SUDO_GID=111 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/18572/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/21484/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -279,7 +311,7 @@ Get: 127 http://deb.debian.org/debian unstable/main i386 python3-pysam i386 0.22.1+ds-2+b2 [4429 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.4-1 [250 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 smalt i386 0.7.6-13 [127 kB] -Fetched 199 MB in 2s (106 MB/s) +Fetched 199 MB in 3s (63.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19956 files and directories currently installed.) @@ -715,8 +747,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Jan 7 13:54:28 UTC 2026. -Universal Time is now: Wed Jan 7 13:54:28 UTC 2026. +Local time is now: Thu Dec 5 07:33:25 UTC 2024. +Universal Time is now: Thu Dec 5 07:33:25 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libio-string-perl (1.08-4) ... @@ -1018,7 +1050,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/iva-1.0.11+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 > ../iva_1.0.11+ds-6_source.changes +I: user script /srv/workspace/pbuilder/21484/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/21484/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/iva-1.0.11+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 > ../iva_1.0.11+ds-6_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-6 dpkg-buildpackage: info: source distribution unstable @@ -1063,15 +1099,15 @@ chmod a+x scripts/* javac -verbose /build/reproducible-path/iva-1.0.11+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.java]] -[parsing completed 38ms] +[parsing completed 237ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] -[parsing completed 3ms] +[parsing completed 12ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] -[parsing completed 2ms] +[parsing completed 3ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] -[parsing completed 12ms] +[parsing completed 36ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] -[parsing completed 16ms] +[parsing completed 53ms] [loading /modules/java.base/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.jartool/module-info.class] @@ -1252,7 +1288,7 @@ [checking getScaffoldStats] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.class] -[total 605ms] +[total 2680ms] Note: /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. dh_auto_build -- @@ -1272,69 +1308,69 @@ running build running build_py creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva -copying iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva +copying iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt -copying iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt -copying iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt -copying iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt -copying iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt +copying iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt +copying iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt +copying iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt +copying iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data -copying iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data +copying iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data +copying iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data -copying iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data running build_scripts creating build/scripts-3.12 -copying and adjusting scripts/iva_qc -> build/scripts-3.12 copying and adjusting scripts/iva -> build/scripts-3.12 +copying and adjusting scripts/iva_qc -> build/scripts-3.12 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.12 -changing mode of build/scripts-3.12/iva_qc from 644 to 755 changing mode of build/scripts-3.12/iva from 644 to 755 +changing mode of build/scripts-3.12/iva_qc from 644 to 755 changing mode of build/scripts-3.12/iva_qc_make_db from 644 to 755 make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' debian/rules override_dh_auto_test @@ -1510,7 +1546,7 @@ =============================== warnings summary =============================== ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 - /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'} + /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'} __version__ = Distribution().from_name('pyfastaq').version iva/test_data_runner.py:20 @@ -1518,7 +1554,7 @@ class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -======================= 160 passed, 2 warnings in 2.75s ======================== +======================= 160 passed, 2 warnings in 13.76s ======================= make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1553,96 +1589,96 @@ self.initialize_options() running build running build_py -copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage -copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage +copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage running build_scripts running install_lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage +copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kcount.py to kcount.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/egg_extract.py to egg_extract.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/edge.py to edge.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/common.py to common.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc.py to qc.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc_external.py to qc_external.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/contig_trim.py to contig_trim.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim.py to read_trim.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/graph.py to graph.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/mapping.py to mapping.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/contig.py to contig.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc_external.py to qc_external.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/edge.py to edge.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed.py to seed.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/mapping.py to mapping.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed_processor.py to seed_processor.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/graph.py to graph.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/egg_extract.py to egg_extract.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/assembly.py to assembly.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/mummer.py to mummer.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kmers.py to kmers.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kcount.py to kcount.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim.py to read_trim.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/external_progs.py to external_progs.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed_processor.py to seed_processor.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kraken.py to kraken.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/common.py to common.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc.py to qc.cpython-312.pyc -byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed.py to seed.cpython-312.pyc +byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kmers.py to kmers.cpython-312.pyc running install_egg_info running egg_info creating iva.egg-info @@ -1659,11 +1695,11 @@ Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin -copying build/scripts-3.12/iva_qc -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.12/iva -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin +copying build/scripts-3.12/iva_qc -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.12/iva_qc_make_db -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin -changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755 changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva to 755 +changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755 changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild @@ -1705,12 +1741,14 @@ 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/21484/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21484/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/18572 and its subdirectories -I: Current time: Wed Jan 7 01:54:54 -12 2026 -I: pbuilder-time-stamp: 1767794094 +I: removing directory /srv/workspace/pbuilder/21484 and its subdirectories +I: Current time: Thu Dec 5 21:34:59 +14 2024 +I: pbuilder-time-stamp: 1733384099