Diff of the two buildlogs: -- --- b1/build.log 2025-07-04 03:14:12.923365216 +0000 +++ b2/build.log 2025-07-04 03:20:57.630073180 +0000 @@ -1,7 +1,6 @@ -W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 3 15:10:07 -12 2025 -I: pbuilder-time-stamp: 1751598607 +I: Current time: Thu Aug 6 23:37:15 +14 2026 +I: pbuilder-time-stamp: 1786009035 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,51 +31,84 @@ dpkg-source: info: applying pr1452.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/469395/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1585914/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Aug 6 09:37 /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/1585914/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1585914/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='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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + 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='469395' - PS1='# ' - PS2='> ' + INVOCATION_ID=996a4b450ae345589b0bbfbeca22d9a5 + 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=1585914 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.JcHweNLA/pbuilderrc_VTcs --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.JcHweNLA/b1 --logfile b1/build.log python-cobra_0.29.1-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/sbin/chroot' - http_proxy='http://192.168.101.4:3128' + 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.JcHweNLA/pbuilderrc_gCiY --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.JcHweNLA/b2 --logfile b2/build.log python-cobra_0.29.1-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/469395/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1585914/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -384,7 +416,7 @@ Get: 216 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 217 http://deb.debian.org/debian unstable/main arm64 python3-sbml5 arm64 5.20.4+dfsg-0.1 [3114 kB] Get: 218 http://deb.debian.org/debian unstable/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB] -Fetched 145 MB in 3s (57.3 MB/s) +Fetched 145 MB in 1s (191 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-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 ... 19963 files and directories currently installed.) @@ -1083,8 +1115,8 @@ Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jul 4 03:10:45 UTC 2025. -Universal Time is now: Fri Jul 4 03:10:45 UTC 2025. +Local time is now: Thu Aug 6 09:38:36 UTC 2026. +Universal Time is now: Thu Aug 6 09:38:36 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1297,7 +1329,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/python-cobra-0.29.1/ && 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 > ../python-cobra_0.29.1-3_source.changes +I: user script /srv/workspace/pbuilder/1585914/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1585914/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-cobra-0.29.1/ && 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 > ../python-cobra_0.29.1-3_source.changes dpkg-buildpackage: info: source package python-cobra dpkg-buildpackage: info: source version 0.29.1-3 dpkg-buildpackage: info: source distribution unstable @@ -1709,46 +1745,46 @@ -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ------------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests ------------------------------------------------------------------------------------------------------------------------- -Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -test_subtract_metabolite_benchmark[glpk] 2.4398 (1.0) 25.6400 (1.0) 2.5585 (1.01) 0.5245 (1.29) 2.5202 (1.00) 0.0400 (1.0) 14;140 390,853.9666 (0.99) 4172 1 -test_subtract_metabolite_benchmark[gurobi] 2.4398 (1.0) 26.3201 (1.03) 2.5379 (1.0) 0.5674 (1.39) 2.5199 (1.0) 0.0799 (1.99) 13;49 394,024.6447 (1.0) 4229 1 -test_subtract_metabolite_benchmark[cplex] 2.4799 (1.02) 27.6000 (1.08) 2.5677 (1.01) 0.4072 (1.0) 2.5600 (1.02) 0.0403 (1.01) 11;337 389,447.3790 (0.99) 4329 1 -test_achr_sample_benchmark 176.1611 (72.20) 319.4020 (12.46) 185.1767 (72.96) 12.9726 (31.86) 181.2412 (71.92) 3.3201 (82.91) 101;143 5,400.2471 (0.01) 1131 1 -test_change_objective_benchmark[optlang-glpk] 230.7610 (94.58) 930.3261 (36.28) 250.6361 (98.76) 43.6058 (107.08) 241.6819 (95.91) 8.4688 (211.47) 125;344 3,989.8475 (0.01) 2491 1 -test_optgp_sample_benchmark 271.5620 (111.30) 414.7619 (16.18) 282.3400 (111.25) 15.8563 (38.94) 276.5211 (109.73) 4.3600 (108.87) 161;246 3,541.8284 (0.01) 1474 1 -test_loopless_benchmark_after 1,380.5688 (565.85) 1,839.1730 (71.73) 1,502.2912 (591.94) 69.2170 (169.98) 1,490.5495 (591.51) 91.7199 (>1000.0) 80;3 665.6499 (0.00) 282 1 -test_loopless_benchmark_before 5,647.4369 (>1000.0) 6,062.2001 (236.44) 5,796.7710 (>1000.0) 75.2596 (184.82) 5,787.6380 (>1000.0) 104.2807 (>1000.0) 33;2 172.5098 (0.00) 100 1 -test_minimal_medium_mip_benchmark 7,709.5309 (>1000.0) 8,336.4150 (325.13) 8,033.4999 (>1000.0) 130.2203 (319.79) 8,038.3130 (>1000.0) 175.7016 (>1000.0) 25;0 124.4787 (0.00) 80 1 -test_minimal_medium_linear_benchmark 8,075.6941 (>1000.0) 9,033.1391 (352.31) 8,336.3164 (>1000.0) 182.5853 (448.38) 8,282.0550 (>1000.0) 219.2815 (>1000.0) 16;3 119.9571 (0.00) 80 1 -test_copy_benchmark[optlang-glpk] 13,657.6500 (>1000.0) 415,383.0579 (>1000.0) 21,227.7697 (>1000.0) 47,589.2479 (>1000.0) 14,050.8520 (>1000.0) 418.9420 (>1000.0) 1;12 47.1081 (0.00) 71 1 -test_gpr_equality_benchmark 18,791.2039 (>1000.0) 19,375.1671 (755.66) 19,005.8304 (>1000.0) 152.4657 (374.42) 18,954.0051 (>1000.0) 191.6213 (>1000.0) 10;0 52.6154 (0.00) 43 1 -test_deepcopy_benchmark 22,873.9111 (>1000.0) 633,229.1341 (>1000.0) 39,375.4169 (>1000.0) 90,630.7261 (>1000.0) 23,698.9160 (>1000.0) 7,396.0387 (>1000.0) 1;1 25.3966 (0.00) 45 1 -test_single_reaction_deletion_benchmark[glpk] 24,359.8409 (>1000.0) 25,110.2862 (979.34) 24,651.2845 (>1000.0) 176.2563 (432.84) 24,622.1621 (>1000.0) 160.3013 (>1000.0) 9;3 40.5658 (0.00) 39 1 -test_fastcc_benchmark[glpk] 60,980.0420 (>1000.0) 61,769.1269 (>1000.0) 61,429.9568 (>1000.0) 316.6291 (777.56) 61,406.5251 (>1000.0) 485.8127 (>1000.0) 2;0 16.2787 (0.00) 5 1 -test_add_metabolite_benchmark[cplex] 64,516.1050 (>1000.0) 64,877.0279 (>1000.0) 64,712.1765 (>1000.0) 104.0890 (255.62) 64,720.0064 (>1000.0) 111.1205 (>1000.0) 6;0 15.4530 (0.00) 16 1 -test_add_metabolite_benchmark[gurobi] 64,741.9058 (>1000.0) 65,035.0680 (>1000.0) 64,832.6299 (>1000.0) 91.5332 (224.78) 64,801.4070 (>1000.0) 71.1601 (>1000.0) 3;3 15.4243 (0.00) 16 1 -test_add_metabolite_benchmark[glpk] 64,954.5889 (>1000.0) 65,243.9101 (>1000.0) 65,044.3588 (>1000.0) 79.3361 (194.83) 65,026.9090 (>1000.0) 118.4409 (>1000.0) 4;0 15.3741 (0.00) 16 1 -test_optgp_init_benchmark 112,251.3800 (>1000.0) 124,900.5431 (>1000.0) 114,247.2373 (>1000.0) 4,048.0027 (>1000.0) 112,945.1441 (>1000.0) 1,072.6672 (>1000.0) 1;1 8.7529 (0.00) 9 1 -test_gpr_symbolism_benchmark 113,348.6270 (>1000.0) 120,996.5979 (>1000.0) 115,240.6751 (>1000.0) 2,392.4370 (>1000.0) 114,423.7539 (>1000.0) 1,772.9725 (>1000.0) 1;1 8.6775 (0.00) 9 1 -test_achr_init_benchmark 113,542.9891 (>1000.0) 123,508.6538 (>1000.0) 115,851.3315 (>1000.0) 4,294.0866 (>1000.0) 113,909.8310 (>1000.0) 2,987.5592 (>1000.0) 1;1 8.6318 (0.00) 5 1 -test_single_gene_deletion_linear_moma_benchmark[glpk] 174,659.7111 (>1000.0) 193,185.4729 (>1000.0) 178,939.5874 (>1000.0) 7,994.2084 (>1000.0) 175,211.8350 (>1000.0) 5,698.8779 (>1000.0) 1;1 5.5885 (0.00) 5 1 -test_double_gene_deletion_benchmark 247,891.9139 (>1000.0) 258,865.2258 (>1000.0) 252,359.7991 (>1000.0) 4,562.6034 (>1000.0) 253,135.6681 (>1000.0) 7,042.2364 (>1000.0) 1;0 3.9626 (0.00) 5 1 -test_single_gene_deletion_linear_room_benchmark[glpk] 249,042.8421 (>1000.0) 268,278.9278 (>1000.0) 254,085.1626 (>1000.0) 8,005.2637 (>1000.0) 251,332.1759 (>1000.0) 6,063.9895 (>1000.0) 1;1 3.9357 (0.00) 5 1 -test_pfba_benchmark[glpk] 297,212.2780 (>1000.0) 645,211.7730 (>1000.0) 369,122.1608 (>1000.0) 154,349.6131 (>1000.0) 301,381.9470 (>1000.0) 88,536.8141 (>1000.0) 1;1 2.7091 (0.00) 5 1 -test_single_gene_deletion_fba_benchmark[glpk] 310,628.3671 (>1000.0) 401,434.9252 (>1000.0) 370,927.8605 (>1000.0) 35,997.0670 (>1000.0) 381,207.0321 (>1000.0) 41,687.1739 (>1000.0) 1;0 2.6959 (0.00) 5 1 -test_flux_variability_loopless_benchmark[glpk] 316,031.1629 (>1000.0) 412,091.4759 (>1000.0) 366,256.7740 (>1000.0) 35,005.8066 (>1000.0) 367,889.4250 (>1000.0) 41,499.0736 (>1000.0) 2;0 2.7303 (0.00) 5 1 -test_copy_benchmark_large_model[optlang-glpk] 327,442.1978 (>1000.0) 858,966.5010 (>1000.0) 528,546.9635 (>1000.0) 271,361.9430 (>1000.0) 335,981.4549 (>1000.0) 477,958.0499 (>1000.0) 1;0 1.8920 (0.00) 5 1 -test_geometric_fba_benchmark[glpk] 387,236.5120 (>1000.0) 403,402.4191 (>1000.0) 391,716.4698 (>1000.0) 6,634.3569 (>1000.0) 389,429.4470 (>1000.0) 5,578.0565 (>1000.0) 1;1 2.5529 (0.00) 5 1 -test_flux_variability_benchmark[glpk] 461,867.2042 (>1000.0) 463,123.0528 (>1000.0) 462,292.4308 (>1000.0) 508.6199 (>1000.0) 462,092.2450 (>1000.0) 654.1951 (>1000.0) 1;0 2.1631 (0.00) 5 1 -test_double_reaction_deletion_benchmark 1,032,704.3261 (>1000.0) 1,701,265.8920 (>1000.0) 1,416,021.3881 (>1000.0) 277,961.5759 (>1000.0) 1,452,011.3692 (>1000.0) 462,476.1679 (>1000.0) 2;0 0.7062 (0.00) 5 1 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +---------------------------------------------------------------------------------------------------------------------- benchmark: 31 tests ----------------------------------------------------------------------------------------------------------------------- +Name (time in us) Min Max Mean StdDev Median IQR Outliers OPS Rounds Iterations +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +test_subtract_metabolite_benchmark[gurobi] 2.3998 (1.0) 305.4000 (15.12) 2.6427 (1.04) 5.0407 (8.83) 2.5199 (1.0) 0.0799 (1.0) 7;78 378,396.9963 (0.96) 3803 1 +test_subtract_metabolite_benchmark[glpk] 2.4000 (1.00) 20.2002 (1.0) 2.5412 (1.0) 0.5707 (1.0) 2.5199 (1.0) 0.0799 (1.0) 11;49 393,514.0945 (1.0) 3001 1 +test_subtract_metabolite_benchmark[cplex] 2.4398 (1.02) 572.5999 (28.35) 2.7173 (1.07) 9.3093 (16.31) 2.5199 (1.0) 0.0799 (1.0) 6;88 368,007.8432 (0.94) 3811 1 +test_achr_sample_benchmark 189.2000 (78.84) 738.8000 (36.57) 238.9472 (94.03) 111.2047 (194.87) 204.1599 (81.02) 32.1701 (402.83) 2;3 4,185.0249 (0.01) 25 1 +test_change_objective_benchmark[optlang-glpk] 230.2402 (95.94) 2,138.4798 (105.86) 277.9364 (109.37) 100.6997 (176.46) 262.8400 (104.30) 20.3399 (254.69) 36;150 3,597.9449 (0.01) 2509 1 +test_optgp_sample_benchmark 295.4800 (123.13) 1,119.2800 (55.41) 338.4685 (133.19) 73.2372 (128.34) 309.5000 (122.82) 33.5199 (419.73) 148;159 2,954.4850 (0.01) 1318 1 +test_loopless_benchmark_after 1,378.3600 (574.37) 4,147.9198 (205.34) 1,654.3531 (651.01) 408.2987 (715.48) 1,512.3601 (600.16) 162.3100 (>1000.0) 28;38 604.4659 (0.00) 285 1 +test_loopless_benchmark_before 5,923.3201 (>1000.0) 7,489.2798 (370.75) 6,609.2510 (>1000.0) 478.2271 (838.02) 6,563.2001 (>1000.0) 676.5801 (>1000.0) 3;0 151.3031 (0.00) 11 1 +test_minimal_medium_mip_benchmark 8,901.4401 (>1000.0) 12,187.4001 (603.33) 9,820.0535 (>1000.0) 587.1722 (>1000.0) 9,693.4601 (>1000.0) 461.0800 (>1000.0) 13;7 101.8324 (0.00) 68 1 +test_minimal_medium_linear_benchmark 9,598.7201 (>1000.0) 11,316.0799 (560.20) 10,128.4269 (>1000.0) 290.7321 (509.46) 10,077.1800 (>1000.0) 281.7200 (>1000.0) 12;4 98.7320 (0.00) 64 1 +test_copy_benchmark[optlang-glpk] 13,957.4399 (>1000.0) 430,486.4800 (>1000.0) 26,176.4260 (>1000.0) 53,551.9109 (>1000.0) 14,957.2800 (>1000.0) 9,753.8200 (>1000.0) 1;1 38.2023 (0.00) 60 1 +test_gpr_equality_benchmark 19,561.6400 (>1000.0) 25,506.4399 (>1000.0) 21,309.6656 (>1000.0) 1,227.2627 (>1000.0) 21,220.4799 (>1000.0) 1,546.2899 (>1000.0) 12;1 46.9271 (0.00) 39 1 +test_deepcopy_benchmark 23,444.7601 (>1000.0) 52,445.4801 (>1000.0) 34,695.1360 (>1000.0) 12,838.2326 (>1000.0) 26,922.1198 (>1000.0) 20,515.0101 (>1000.0) 1;0 28.8225 (0.00) 5 1 +test_single_reaction_deletion_benchmark[glpk] 25,943.3598 (>1000.0) 48,856.2000 (>1000.0) 30,525.7550 (>1000.0) 4,682.8092 (>1000.0) 29,314.9200 (>1000.0) 2,936.7200 (>1000.0) 2;2 32.7592 (0.00) 24 1 +test_fastcc_benchmark[glpk] 62,037.4400 (>1000.0) 89,766.1599 (>1000.0) 70,454.9025 (>1000.0) 10,370.8163 (>1000.0) 65,749.5800 (>1000.0) 10,516.4400 (>1000.0) 4;0 14.1935 (0.00) 16 1 +test_add_metabolite_benchmark[glpk] 69,656.1199 (>1000.0) 169,039.2401 (>1000.0) 124,010.3200 (>1000.0) 41,965.3282 (>1000.0) 128,897.7999 (>1000.0) 79,061.1300 (>1000.0) 3;0 8.0638 (0.00) 7 1 +test_add_metabolite_benchmark[gurobi] 69,684.8400 (>1000.0) 171,104.6800 (>1000.0) 140,039.1314 (>1000.0) 45,592.5897 (>1000.0) 164,792.5200 (>1000.0) 70,281.7499 (>1000.0) 2;0 7.1409 (0.00) 7 1 +test_add_metabolite_benchmark[cplex] 75,951.4000 (>1000.0) 182,374.0399 (>1000.0) 122,822.1600 (>1000.0) 43,746.9698 (>1000.0) 107,186.3001 (>1000.0) 86,636.1598 (>1000.0) 6;0 8.1419 (0.00) 14 1 +test_optgp_init_benchmark 122,661.1601 (>1000.0) 311,979.5199 (>1000.0) 218,083.9300 (>1000.0) 85,403.4026 (>1000.0) 239,783.5799 (>1000.0) 167,030.9200 (>1000.0) 4;0 4.5854 (0.00) 8 1 +test_achr_init_benchmark 122,853.6400 (>1000.0) 157,588.5601 (>1000.0) 130,257.2241 (>1000.0) 15,284.4945 (>1000.0) 123,411.6801 (>1000.0) 9,175.0100 (>1000.0) 1;1 7.6771 (0.00) 5 1 +test_gpr_symbolism_benchmark 129,286.8799 (>1000.0) 270,119.2000 (>1000.0) 154,989.8950 (>1000.0) 47,774.7730 (>1000.0) 134,201.6800 (>1000.0) 24,483.9400 (>1000.0) 1;1 6.4520 (0.00) 8 1 +test_single_gene_deletion_linear_moma_benchmark[glpk] 184,054.8401 (>1000.0) 1,194,448.5200 (>1000.0) 393,667.5841 (>1000.0) 447,763.7335 (>1000.0) 189,958.6001 (>1000.0) 268,407.7900 (>1000.0) 1;1 2.5402 (0.00) 5 1 +test_flux_variability_loopless_benchmark[glpk] 241,448.8001 (>1000.0) 283,160.6001 (>1000.0) 258,639.7600 (>1000.0) 17,276.2195 (>1000.0) 255,805.0000 (>1000.0) 28,142.2900 (>1000.0) 1;0 3.8664 (0.00) 5 1 +test_double_gene_deletion_benchmark 260,049.6002 (>1000.0) 280,096.5598 (>1000.0) 268,166.3120 (>1000.0) 7,335.5269 (>1000.0) 267,451.2800 (>1000.0) 6,401.3100 (>1000.0) 2;0 3.7290 (0.00) 5 1 +test_single_gene_deletion_linear_room_benchmark[glpk] 275,069.0400 (>1000.0) 420,795.6798 (>1000.0) 350,998.9280 (>1000.0) 61,180.7984 (>1000.0) 355,390.2400 (>1000.0) 106,101.9799 (>1000.0) 2;0 2.8490 (0.00) 5 1 +test_pfba_benchmark[glpk] 307,638.3199 (>1000.0) 313,213.2799 (>1000.0) 310,646.8960 (>1000.0) 2,458.9817 (>1000.0) 309,979.3200 (>1000.0) 4,295.9700 (>1000.0) 3;0 3.2191 (0.00) 5 1 +test_single_gene_deletion_fba_benchmark[glpk] 325,208.8800 (>1000.0) 402,960.3601 (>1000.0) 351,630.9920 (>1000.0) 31,749.2262 (>1000.0) 334,873.5999 (>1000.0) 40,254.9599 (>1000.0) 1;0 2.8439 (0.00) 5 1 +test_copy_benchmark_large_model[optlang-glpk] 340,114.7600 (>1000.0) 953,121.6798 (>1000.0) 600,350.5680 (>1000.0) 309,161.7379 (>1000.0) 445,043.6002 (>1000.0) 582,869.3700 (>1000.0) 2;0 1.6657 (0.00) 5 1 +test_geometric_fba_benchmark[glpk] 461,681.5199 (>1000.0) 492,354.0000 (>1000.0) 476,293.2000 (>1000.0) 11,505.5272 (>1000.0) 473,472.4401 (>1000.0) 15,104.9100 (>1000.0) 2;0 2.0995 (0.00) 5 1 +test_flux_variability_benchmark[glpk] 483,256.3999 (>1000.0) 519,818.8401 (>1000.0) 502,985.6080 (>1000.0) 16,693.1589 (>1000.0) 503,972.9599 (>1000.0) 31,370.2502 (>1000.0) 2;0 1.9881 (0.00) 5 1 +test_double_reaction_deletion_benchmark 897,876.5600 (>1000.0) 1,163,447.6800 (>1000.0) 1,008,129.2000 (>1000.0) 99,049.5872 (>1000.0) 995,700.9999 (>1000.0) 117,002.3900 (>1000.0) 2;0 0.9919 (0.00) 5 1 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Legend: Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile. OPS: Operations Per Second, computed as 1 / Mean -==== 516 passed, 27 skipped, 11 xfailed, 5494 warnings in 134.09s (0:02:14) ==== +==== 516 passed, 27 skipped, 11 xfailed, 5494 warnings in 155.78s (0:02:35) ==== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -2060,8 +2096,8 @@ dpkg-gencontrol: warning: Depends field of package python3-cobra: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-cobra' in '../python3-cobra_0.29.1-3_arm64.deb'. dpkg-deb: building package 'python-cobra-data' in '../python-cobra-data_0.29.1-3_all.deb'. +dpkg-deb: building package 'python3-cobra' in '../python3-cobra_0.29.1-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../python-cobra_0.29.1-3_arm64.buildinfo dpkg-genchanges --build=binary -O../python-cobra_0.29.1-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2069,12 +2105,14 @@ 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/1585914/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1585914/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/469395 and its subdirectories -I: Current time: Thu Jul 3 15:14:11 -12 2025 -I: pbuilder-time-stamp: 1751598851 +I: removing directory /srv/workspace/pbuilder/1585914 and its subdirectories +I: Current time: Thu Aug 6 23:43:56 +14 2026 +I: pbuilder-time-stamp: 1786009436