Diff of the two buildlogs: -- --- b1/build.log 2023-04-18 08:33:09.680393159 +0000 +++ b2/build.log 2023-04-18 08:44:53.493159054 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 17 20:22:28 -12 2023 -I: pbuilder-time-stamp: 1681806148 +I: Current time: Tue May 21 04:57:03 +14 2024 +I: pbuilder-time-stamp: 1716217023 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./bioperl-run_1.7.3.orig.tar.gz] I: copying [./bioperl-run_1.7.3-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Jan 22 01:58:02 2023 -12 +gpgv: Signature made Mon Jan 23 03:58:02 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -47,52 +47,84 @@ dpkg-source: info: applying adjust-muscle-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21760/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3819/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 21 04:57 /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/3819/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3819/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='21760' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3819 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.JOgDaS3g/pbuilderrc_l88W --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.JOgDaS3g/b1 --logfile b1/build.log bioperl-run_1.7.3-9.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JOgDaS3g/pbuilderrc_gVSX --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.JOgDaS3g/b2 --logfile b2/build.log --extrapackages usrmerge bioperl-run_1.7.3-9.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 15 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21760/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 19 06:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3819/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -449,7 +481,7 @@ Get: 236 http://deb.debian.org/debian bookworm/main arm64 tigr-glimmer arm64 3.02b-6+b1 [270 kB] Get: 237 http://deb.debian.org/debian bookworm/main arm64 wise-data all 2.4.1-23 [78.2 kB] Get: 238 http://deb.debian.org/debian bookworm/main arm64 wise arm64 2.4.1-23 [969 kB] -Fetched 169 MB in 22s (7649 kB/s) +Fetched 169 MB in 4s (44.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) @@ -1440,8 +1472,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-9_source.changes +I: user script /srv/workspace/pbuilder/3819/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/3819/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/bioperl-run-1.7.3/ && 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 > ../bioperl-run_1.7.3-9_source.changes dpkg-buildpackage: info: source package bioperl-run dpkg-buildpackage: info: source version 1.7.3-9 dpkg-buildpackage: info: source distribution unstable @@ -1507,7 +1548,7 @@ gapOpen[] = { 0.01993141696 0.01993141696 } gapExtend[] = { 0.7943345308 0.7943345308 } -Loading sequence file: /tmp/ZaDP8XuHy2 +Loading sequence file: /tmp/YZZsC3nXk8 Computing posterior matrices Building DAG Starting the sequence annealing process @@ -1549,7 +1590,7 @@ ok 11 - can return output format for command 'annotate' ok 12 - result claims to be in correct format for command 'annotate' ok 13 - can return output file for command 'annotate' -ok 14 - file format of '/tmp/ldlfuIdrk3/KL_VKen5GS.bed' consistent with claim for 'annotate' +ok 14 - file format of '/tmp/vmjT0jFkzy/Mje5nS7nsI.bed' consistent with claim for 'annotate' ok 15 - can set want to IO object for command 'annotate' ok 16 - can get the basic object result for command 'annotate' ok 17 - 'returned object is correct for command 'annotate'' isa 'Bio::Root::IO' @@ -1586,7 +1627,7 @@ ok 48 - can return output format for command 'overlap' ok 49 - result claims to be in correct format for command 'overlap' ok 50 - can return output file for command 'overlap' -ok 51 - file format of '/tmp/QXW2GDhkhI/L9VKaeq5lT.bed' consistent with claim for 'overlap' +ok 51 - file format of '/tmp/P7z3vzPqCk/goNnPF7VzG.bed' consistent with claim for 'overlap' ok 52 - can set want to IO object for command 'overlap' ok 53 - can get the basic object result for command 'overlap' ok 54 - 'returned object is correct for command 'overlap'' isa 'Bio::Root::IO' @@ -1604,7 +1645,7 @@ ok 66 - can return output format for command 'bam_to_bed' ok 67 - result claims to be in correct format for command 'bam_to_bed' ok 68 - can return output file for command 'bam_to_bed' -ok 69 - file format of '/tmp/eFekuUweZI/1AXuqYhfLe.bed' consistent with claim for 'bam_to_bed' +ok 69 - file format of '/tmp/gOBMDaHnym/mLNopbsRIj.bed' consistent with claim for 'bam_to_bed' ok 70 - can set want to IO object for command 'bam_to_bed' ok 71 - can get the basic object result for command 'bam_to_bed' ok 72 - 'returned object is correct for command 'bam_to_bed'' isa 'Bio::Root::IO' @@ -1639,7 +1680,7 @@ ok 101 - can return output format for command 'pair_to_pair' ok 102 - result claims to be in correct format for command 'pair_to_pair' ok 103 - can return output file for command 'pair_to_pair' -ok 104 - file format of '/tmp/iaBTlYyKaY/uQkVYS3RvP.bedpe' consistent with claim for 'pair_to_pair' +ok 104 - file format of '/tmp/ktaSAPaecV/YLUU5q10st.bedpe' consistent with claim for 'pair_to_pair' ok 105 - can set want to IO object for command 'pair_to_pair' ok 106 - can get the basic object result for command 'pair_to_pair' ok 107 - 'returned object is correct for command 'pair_to_pair'' isa 'Bio::Root::IO' @@ -1719,7 +1760,7 @@ ok 181 - can return output format for command 'group_by' ok 182 - result claims to be in correct format for command 'group_by' ok 183 - can return output file for command 'group_by' -ok 184 - file format of '/tmp/CCrEnSHJnp/NB7xFDSpWV.bed' consistent with claim for 'group_by' +ok 184 - file format of '/tmp/WsW4nu9cYj/7QMqiwttTy.bed' consistent with claim for 'group_by' ok 185 - can set want to IO object for command 'group_by' ok 186 - can get the basic object result for command 'group_by' ok 187 - 'returned object is correct for command 'group_by'' isa 'Bio::Root::IO' @@ -1737,7 +1778,7 @@ ok 199 - can return output format for command 'shuffle' ok 200 - result claims to be in correct format for command 'shuffle' ok 201 - can return output file for command 'shuffle' -ok 202 - file format of '/tmp/laybtAaMs9/P1YOEKugim.bed' consistent with claim for 'shuffle' +ok 202 - file format of '/tmp/0hKAxFwRT5/vmmh300pIc.bed' consistent with claim for 'shuffle' ok 203 - can set want to IO object for command 'shuffle' ok 204 - can get the basic object result for command 'shuffle' ok 205 - 'returned object is correct for command 'shuffle'' isa 'Bio::Root::IO' @@ -1755,7 +1796,7 @@ ok 217 - can return output format for command 'b12_to_b6' ok 218 - result claims to be in correct format for command 'b12_to_b6' ok 219 - can return output file for command 'b12_to_b6' -ok 220 - file format of '/tmp/Ug_7S_sHgP/604AQO05mK.bed' consistent with claim for 'b12_to_b6' +ok 220 - file format of '/tmp/LDDgBYJyAI/RLI9Q_IKlP.bed' consistent with claim for 'b12_to_b6' ok 221 - can set want to IO object for command 'b12_to_b6' ok 222 - can get the basic object result for command 'b12_to_b6' ok 223 - 'returned object is correct for command 'b12_to_b6'' isa 'Bio::Root::IO' @@ -1795,7 +1836,7 @@ ok 253 - can return output format for command 'slop' ok 254 - result claims to be in correct format for command 'slop' ok 255 - can return output file for command 'slop' -ok 256 - file format of '/tmp/btynZEFUpC/KKsEuLyEYE.bed' consistent with claim for 'slop' +ok 256 - file format of '/tmp/AAic1Y8nEf/OMbW1xBcWu.bed' consistent with claim for 'slop' ok 257 - can set want to IO object for command 'slop' ok 258 - can get the basic object result for command 'slop' ok 259 - 'returned object is correct for command 'slop'' isa 'Bio::Root::IO' @@ -1813,7 +1854,7 @@ ok 271 - can return output format for command 'closest' ok 272 - result claims to be in correct format for command 'closest' ok 273 - can return output file for command 'closest' -ok 274 - file format of '/tmp/pE8Aw2zxV8/Z6dG5_GYt1.bedpe' consistent with claim for 'closest' +ok 274 - file format of '/tmp/QsOnPUVjyq/fi8A7ivN4U.bedpe' consistent with claim for 'closest' ok 275 - can set want to IO object for command 'closest' ok 276 - can get the basic object result for command 'closest' ok 277 - 'returned object is correct for command 'closest'' isa 'Bio::Root::IO' @@ -1848,7 +1889,7 @@ ok 306 - can return output format for command 'sort' ok 307 - result claims to be in correct format for command 'sort' ok 308 - can return output file for command 'sort' -ok 309 - file format of '/tmp/G4ndkY9Px1/9xvmo6Wa04.bed' consistent with claim for 'sort' +ok 309 - file format of '/tmp/HmXVWvN2Cz/PutN6IurbD.bed' consistent with claim for 'sort' ok 310 - can set want to IO object for command 'sort' ok 311 - can get the basic object result for command 'sort' ok 312 - 'returned object is correct for command 'sort'' isa 'Bio::Root::IO' @@ -1866,7 +1907,7 @@ ok 324 - can return output format for command 'complement' ok 325 - result claims to be in correct format for command 'complement' ok 326 - can return output file for command 'complement' -ok 327 - file format of '/tmp/SoSbi8kwtd/al9qb3CLoE.bed' consistent with claim for 'complement' +ok 327 - file format of '/tmp/vMk9vLCShS/jcA8WEpYOm.bed' consistent with claim for 'complement' ok 328 - can set want to IO object for command 'complement' ok 329 - can get the basic object result for command 'complement' ok 330 - 'returned object is correct for command 'complement'' isa 'Bio::Root::IO' @@ -1902,7 +1943,7 @@ ok 360 - can return output format for command 'subtract' ok 361 - result claims to be in correct format for command 'subtract' ok 362 - can return output file for command 'subtract' -ok 363 - file format of '/tmp/Agxxpyx7T8/QZNVfSCl0y.bed' consistent with claim for 'subtract' +ok 363 - file format of '/tmp/IFGAin1yN4/ws7fxQBkWv.bed' consistent with claim for 'subtract' ok 364 - can set want to IO object for command 'subtract' ok 365 - can get the basic object result for command 'subtract' ok 366 - 'returned object is correct for command 'subtract'' isa 'Bio::Root::IO' @@ -1924,7 +1965,7 @@ ok 378 - can return output format for command 'coverage' ok 379 - result claims to be in correct format for command 'coverage' ok 380 - can return output file for command 'coverage' -ok 381 - file format of '/tmp/NKylsO6qPz/f7pzeq00ak.bed' consistent with claim for 'coverage' +ok 381 - file format of '/tmp/MA_WRdlO7g/NqivjqelQE.bed' consistent with claim for 'coverage' ok 382 - can set want to IO object for command 'coverage' ok 383 - can get the basic object result for command 'coverage' ok 384 - 'returned object is correct for command 'coverage'' isa 'Bio::Root::IO' @@ -1946,7 +1987,7 @@ ok 396 - can return output format for command 'merge' ok 397 - result claims to be in correct format for command 'merge' ok 398 - can return output file for command 'merge' -ok 399 - file format of '/tmp/3nuPZazKh7/blqD9KMiQA.bed' consistent with claim for 'merge' +ok 399 - file format of '/tmp/IkUjQZuQwP/fX4oPWi548.bed' consistent with claim for 'merge' ok 400 - can set want to IO object for command 'merge' ok 401 - can get the basic object result for command 'merge' ok 402 - 'returned object is correct for command 'merge'' isa 'Bio::Root::IO' @@ -1964,7 +2005,7 @@ ok 414 - can return output format for command 'window' ok 415 - result claims to be in correct format for command 'window' ok 416 - can return output file for command 'window' -ok 417 - file format of '/tmp/HOQWtedaVW/DOY474t33_.bedpe' consistent with claim for 'window' +ok 417 - file format of '/tmp/jjONWjK2Xt/HaRjmSp3nv.bedpe' consistent with claim for 'window' ok 418 - can set want to IO object for command 'window' ok 419 - can get the basic object result for command 'window' ok 420 - 'returned object is correct for command 'window'' isa 'Bio::Root::IO' @@ -2600,15 +2641,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2023-04-17 20:31:12] : LOG : Detected protein sequences. -[2023-04-17 20:31:12] : LOG : Read 7 sequences from standard input. -[2023-04-17 20:31:12] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-04-17 20:31:12] : LOG : Calculating pairwise distances -[2023-04-17 20:31:12] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-04-17 20:31:12] : LOG : Building guide tree. -[2023-04-17 20:31:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:01.00 -[2023-04-17 20:31:13] : LOG : Aligning -[2023-04-17 20:31:13] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Detected protein sequences. +[2024-05-21 05:05:35] : LOG : Read 7 sequences from standard input. +[2024-05-21 05:05:35] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Calculating pairwise distances +[2024-05-21 05:05:35] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Building guide tree. +[2024-05-21 05:05:35] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Aligning +[2024-05-21 05:05:35] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 ok 5 ok 6 @@ -2627,15 +2668,15 @@ Bioinformatics (2019) https://doi.org/10.1093/bioinformatics/btz795 -[2023-04-17 20:31:13] : LOG : Detected protein sequences. -[2023-04-17 20:31:13] : LOG : Read 7 sequences from standard input. -[2023-04-17 20:31:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-04-17 20:31:13] : LOG : Calculating pairwise distances -[2023-04-17 20:31:13] : LOG : CPU Time: 0.01u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-04-17 20:31:13] : LOG : Building guide tree. -[2023-04-17 20:31:13] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 -[2023-04-17 20:31:13] : LOG : Aligning -[2023-04-17 20:31:13] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Detected protein sequences. +[2024-05-21 05:05:35] : LOG : Read 7 sequences from standard input. +[2024-05-21 05:05:35] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Calculating pairwise distances +[2024-05-21 05:05:35] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Building guide tree. +[2024-05-21 05:05:35] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00 +[2024-05-21 05:05:35] : LOG : Aligning +[2024-05-21 05:05:35] : LOG : CPU Time: 0.04u 00:00:00.03 Elapsed: 00:00:00.00 ok 7 ok # Required executable for Bio::Tools::Run::Phylo::LVB is not present @@ -3095,7 +3136,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/7ZKI7re11W +Loading sequence file: /tmp/gXmF41dibl Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3108,7 +3149,7 @@ gapOpen[] = { 0.0119511066 0.0119511066 0.008008334786 0.008008334786 } gapExtend[] = { 0.3965826333 0.3965826333 0.8988758326 0.8988758326 } -Loading sequence file: /tmp/2R39TuIYWx +Loading sequence file: /tmp/ll96KY_AvC Computing posterior matrix: (1) CYS1_DICDI vs. (2) ALEU_HORVU -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (3) CATH_HUMAN -- done. Computing posterior matrix: (1) CYS1_DICDI vs. (4) CATH_RAT -- done. @@ -3144,7 +3185,7 @@ gapOpen[] = { 0.01386308484 0.01386308484 0.006556345616 0.006556345616 } gapExtend[] = { 0.3603379726 0.3603379726 0.7831884027 0.7831884027 } -Loading sequence file: /tmp/6DKxKEShlF +Loading sequence file: /tmp/BSWVLMk79w Alignment tree: ((CYS1_DICDI (CATL_HUMAN CATL_RAT)) ((ALEU_HORVU (CATH_HUMAN CATH_RAT)) PAPA_CARPA)) @@ -3604,7 +3645,7 @@ t/BEDTools.t (Wstat: 0 Tests: 423 Failed: 0) TODO passed: 20, 57, 75, 88, 110, 155, 190, 208, 226 262, 280, 315, 333, 405 -Files=60, Tests=1652, 507 wallclock secs ( 0.80 usr 0.25 sys + 475.82 cusr 24.50 csys = 501.37 CPU) +Files=60, Tests=1652, 503 wallclock secs ( 0.77 usr 0.26 sys + 476.85 cusr 23.92 csys = 501.80 CPU) Result: PASS mv t.skip/* t rm -rf t.skip @@ -3814,11 +3855,11 @@ Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::SoapEUtilities.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap::WSDL.3pm Installing /build/bioperl-run-1.7.3/debian/tmp/usr/share/man/man3/Bio::DB::ESoap.3pm -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl -Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_protdist.pl +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_multi_hmmsearch.pl Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_papplmaker.pl +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_run_neighbor.pl +Installing /build/bioperl-run-1.7.3/debian/tmp/usr/bin/bp_panalysis.pl dh_install dh_installdocs dh_installchangelogs @@ -3843,12 +3884,14 @@ 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/3819/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3819/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/21760 and its subdirectories -I: Current time: Mon Apr 17 20:33:08 -12 2023 -I: pbuilder-time-stamp: 1681806788 +I: removing directory /srv/workspace/pbuilder/3819 and its subdirectories +I: Current time: Tue May 21 05:07:27 +14 2024 +I: pbuilder-time-stamp: 1716217647