Tue Dec 3 05:51:52 UTC 2024 I: starting to build gubbins/trixie/amd64 on jenkins on '2024-12-03 05:51' Tue Dec 3 05:51:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/41258/console.log Tue Dec 3 05:51:52 UTC 2024 I: Downloading source for trixie/gubbins=3.4-1 --2024-12-03 05:51:52-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_3.4-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2406 (2.3K) [text/prs.lines.tag] Saving to: ‘gubbins_3.4-1.dsc’ 0K .. 100% 330M=0s 2024-12-03 05:51:52 (330 MB/s) - ‘gubbins_3.4-1.dsc’ saved [2406/2406] Tue Dec 3 05:51:52 UTC 2024 I: gubbins_3.4-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 3.4-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/gubbins Vcs-Git: https://salsa.debian.org/med-team/gubbins.git Testsuite: autopkgtest Testsuite-Triggers: iqtree Build-Depends: debhelper-compat (= 13), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox , python3-scipy , python3-multiprocess , python3-wheel Package-List: gubbins deb science optional arch=any Checksums-Sha1: 7af60a6e649cebff6772e3089a8eb8578be91198 2878089 gubbins_3.4.orig.tar.gz e0653a7efe37b9040fead72deb64eef41dd9f31c 9624 gubbins_3.4-1.debian.tar.xz Checksums-Sha256: ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d 2878089 gubbins_3.4.orig.tar.gz 7f29b1fbb0735c724186d3664895f08e03e680dc3147e4065e9a81f301213bb9 9624 gubbins_3.4-1.debian.tar.xz Files: 3c8e6a0d6d119a0b535615747cb76b28 2878089 gubbins_3.4.orig.tar.gz 2db4702ddc913d188ecf2d1bea96e6de 9624 gubbins_3.4-1.debian.tar.xz Dgit: a6d56194077d6dcb81dc18906b3d49e41ff20b97 debian archive/debian/3.4-1 https://git.dgit.debian.org/gubbins -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmdLVdMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqVOA//bvyn/b9xtKMSzZVd/899hbSHqS3m BxjRARGOkuL3DLxW/8Q3tiZafI1Xbk6GmhcOHXfLlA9SEGj8TioLUObDoBxSWXn2 dU7dk+DKEOmFPfN3Zgwno+YHGZOqw2vHUiFBIdX5yk3s+QaVVEA0YYH/C9zY4tk2 73dP1pPWyMA3/gjyVgGivXA0I68aKP43zyM65yR/stuIoE1BX5iWMxrTDLqaSp2n Rwe5OPe0S+OorvHzSPt8nPHNzJwNsCLA/3l/wXKLsf4d+IzKIs15V30uAXRXP0u5 +lgOe3RfrVf6gpMmsm6axGWgZBNPCHkPwzbk75EUnsKLAxlEylVs4+7ajPBIMX5D i5topNCVfzZfBGZPFqVPShyfN9/OHYsS3Zl/3WB2Du0/dWwIC8PmmTOJS1fDoTEr q+eGuwTVeCv9zGkbCM8cLRf94yxCJPrr6FwQDBYQU1Va9UZ/6iX79+WRHNxAUncX V2jBYJ+Dy7mAW28Dym0uS+t40LLA08HMMV5XWMuWwEKxvhMwxlZ6ckFnlZeRE+3b tNcY5+PzB5HI4nqyY4+eDIlVcd/p/UTU9C/0frwBSv10pdvDIl93EpmpMPPV/L0P q/sRAUYofm+NkF7pVgbCOzKnw+udTqHgx8jpOmL9xT4djSnSLejKzhxXH9cFC+8X TjnxyElF+EPyfkw= =fhy5 -----END PGP SIGNATURE----- Tue Dec 3 05:51:52 UTC 2024 I: Checking whether the package is not for us Tue Dec 3 05:51:52 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Dec 3 05:51:52 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Dec 3 05:54:04 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 5 00:14:53 -12 2026 I: pbuilder-time-stamp: 1767615293 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] tar: ./build: time stamp 2027-02-01 12:10:44 is 33911750.172429112 s in the future tar: ./dev/ptmx: time stamp 2027-02-01 12:09:31 is 33911677.172089723 s in the future tar: ./dev/zero: time stamp 2027-02-01 12:09:31 is 33911677.171930962 s in the future tar: ./dev/null: time stamp 2027-02-01 12:09:31 is 33911677.17186858 s in the future tar: ./dev/console: time stamp 2027-02-01 12:09:31 is 33911677.171811365 s in the future tar: ./dev/random: time stamp 2027-02-01 12:09:31 is 33911677.171776271 s in the future tar: ./dev/full: time stamp 2027-02-01 12:09:31 is 33911677.171743335 s in the future tar: ./dev/pts: time stamp 2027-02-01 12:09:31 is 33911677.171686562 s in the future tar: ./dev/tty: time stamp 2027-02-01 12:09:31 is 33911677.171635245 s in the future tar: ./dev/urandom: time stamp 2027-02-01 12:09:31 is 33911677.17160267 s in the future tar: ./etc/terminfo: time stamp 2027-02-01 12:10:00 is 33911706.171372232 s in the future tar: ./etc/opt: time stamp 2027-02-01 12:09:32 is 33911678.169921122 s in the future tar: ./etc/security/opasswd: time stamp 2027-02-01 12:10:03 is 33911709.169549836 s in the future tar: ./etc/security: time stamp 2027-02-01 12:10:03 is 33911709.169231443 s in the future tar: ./etc/shadow: time stamp 2027-02-01 12:10:54 is 33911760.168942882 s in the future tar: ./etc/apt/apt.conf.d/80proxy: time stamp 2027-02-01 12:12:07 is 33911833.168536046 s in the future tar: ./etc/apt/apt.conf.d/15pbuilder: time stamp 2027-02-01 12:10:44 is 33911750.168456443 s in the future tar: ./etc/apt/sources.list: time stamp 2027-02-01 12:12:08 is 33911834.168161074 s in the future tar: ./etc/apt/trusted.gpg.d: time stamp 2027-02-01 12:10:30 is 33911736.167556086 s in the future tar: ./etc/apt: time stamp 2027-02-01 12:12:08 is 33911834.16743328 s in the future tar: ./etc/fstab: time stamp 2027-02-01 12:09:31 is 33911677.167369853 s in the future tar: ./etc/ld.so.conf.d: time stamp 2027-02-01 12:11:20 is 33911786.166544052 s in the future tar: ./etc/gshadow: time stamp 2027-02-01 12:10:54 is 33911760.166368292 s in the future tar: ./etc/shells: time stamp 2027-02-01 12:10:00 is 33911706.166272947 s in the future tar: ./etc/default: time stamp 2027-02-01 12:10:54 is 33911760.165982964 s in the future tar: ./etc/group: time stamp 2027-02-01 12:10:54 is 33911760.165840756 s in the future tar: ./etc/.pwd.lock: time stamp 2027-02-01 12:10:54 is 33911760.165492338 s in the future tar: ./etc/skel: time stamp 2027-02-01 12:10:01 is 33911707.165276697 s in the future tar: ./etc/group-: time stamp 2027-02-01 12:09:31 is 33911677.165141144 s in the future tar: ./etc/subuid: time stamp 2027-02-01 12:09:31 is 33911677.165075667 s in the future tar: ./etc/pam.d/common-session: time stamp 2027-02-01 12:10:03 is 33911709.164149948 s in the future tar: ./etc/pam.d/common-password: time stamp 2027-02-01 12:10:03 is 33911709.164043662 s in the future tar: ./etc/pam.d/common-account: time stamp 2027-02-01 12:10:03 is 33911709.163960746 s in the future tar: ./etc/pam.d/common-session-noninteractive: time stamp 2027-02-01 12:10:03 is 33911709.163832204 s in the future tar: ./etc/pam.d/common-auth: time stamp 2027-02-01 12:10:03 is 33911709.163714842 s in the future tar: ./etc/pam.d: time stamp 2027-02-01 12:10:54 is 33911760.163453002 s in the future tar: ./etc/subgid: time stamp 2027-02-01 12:09:31 is 33911677.163317915 s in the future tar: ./etc/passwd-: time stamp 2027-02-01 12:09:31 is 33911677.163218807 s in the future tar: ./etc/environment: time stamp 2027-02-01 12:10:03 is 33911709.163087104 s in the future tar: ./etc/perl: time stamp 2027-02-01 12:10:29 is 33911735.162914237 s in the future tar: ./etc/selinux: time stamp 2027-02-01 12:10:53 is 33911759.162698184 s in the future tar: ./etc/kernel: time stamp 2027-02-01 12:10:06 is 33911712.162521185 s in the future tar: ./etc/passwd: time stamp 2027-02-01 12:10:54 is 33911760.162433474 s in the future tar: ./etc/dpkg/origins/default: time stamp 2027-02-01 12:09:32 is 33911678.162211945 s in the future tar: ./etc/dpkg/dpkg.cfg.d/02speedup: time stamp 2027-02-01 12:12:08 is 33911834.161854706 s in the future tar: ./etc/dpkg/dpkg.cfg.d: time stamp 2027-02-01 12:12:08 is 33911834.161815817 s in the future tar: ./etc/dpkg: time stamp 2027-02-01 12:10:37 is 33911743.161781006 s in the future tar: ./media: time stamp 2027-02-01 12:09:32 is 33911678.161435377 s in the future tar: ./mnt: time stamp 2027-02-01 12:09:32 is 33911678.161351265 s in the future tar: ./opt: time stamp 2027-02-01 12:09:32 is 33911678.161278131 s in the future tar: ./root: time stamp 2027-02-01 12:09:32 is 33911678.161011551 s in the future tar: ./run/lock: time stamp 2027-02-01 12:09:32 is 33911678.160876882 s in the future tar: ./srv: time stamp 2027-02-01 12:09:32 is 33911678.160771677 s in the future tar: ./usr/share/base-passwd: time stamp 2027-02-01 12:09:42 is 33911688.160312513 s in the future tar: ./usr/share/terminfo/a: time stamp 2027-02-01 12:09:57 is 33911703.160083745 s in the future tar: ./usr/share/terminfo/p: time stamp 2027-02-01 12:09:57 is 33911703.159930532 s in the future tar: ./usr/share/terminfo/E: time stamp 2027-02-01 12:09:57 is 33911703.159741504 s in the future tar: ./usr/share/terminfo/s: time stamp 2027-02-01 12:09:57 is 33911703.159237982 s in the future tar: ./usr/share/terminfo/h: time stamp 2027-02-01 12:09:57 is 33911703.159107147 s in the future tar: ./usr/share/terminfo/d: time stamp 2027-02-01 12:09:57 is 33911703.159001373 s in the future tar: ./usr/share/terminfo/l: time stamp 2027-02-01 12:09:57 is 33911703.158829904 s in the future tar: ./usr/share/terminfo/m: time stamp 2027-02-01 12:09:57 is 33911703.158462973 s in the future tar: ./usr/share/terminfo/c: time stamp 2027-02-01 12:09:57 is 33911703.158246664 s in the future tar: ./usr/share/terminfo/v: time stamp 2027-02-01 12:09:57 is 33911703.157945027 s in the future tar: ./usr/share/terminfo/w: time stamp 2027-02-01 12:09:57 is 33911703.157777061 s in the future tar: ./usr/share/terminfo/x: time stamp 2027-02-01 12:09:57 is 33911703.157217418 s in the future tar: ./usr/share/terminfo/t: time stamp 2027-02-01 12:09:57 is 33911703.157005895 s in the future tar: ./usr/share/terminfo/r: time stamp 2027-02-01 12:09:57 is 33911703.156658363 s in the future tar: ./usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu: time stamp 2027-02-01 12:10:27 is 33911733.156222422 s in the future tar: ./usr/share/gdb/auto-load/usr/lib: time stamp 2027-02-01 12:10:24 is 33911730.156181557 s in the future tar: ./usr/share/gdb/auto-load/usr: time stamp 2027-02-01 12:10:24 is 33911730.156156446 s in the future tar: ./usr/share/gdb/auto-load/lib/x86_64-linux-gnu: time stamp 2027-02-01 12:10:21 is 33911727.155972499 s in the future tar: ./usr/share/gdb/auto-load/lib: time stamp 2027-02-01 12:10:21 is 33911727.155943476 s in the future tar: ./usr/share/gdb/auto-load: time stamp 2027-02-01 12:10:24 is 33911730.155921163 s in the future tar: ./usr/share/gdb: time stamp 2027-02-01 12:10:21 is 33911727.155899981 s in the future tar: ./usr/share/info: time stamp 2027-02-01 12:09:59 is 33911705.15093056 s in the future tar: ./usr/share/build-essential: time stamp 2027-02-01 12:10:11 is 33911717.150745365 s in the future tar: ./usr/share/libc-bin: time stamp 2027-02-01 12:09:51 is 33911697.150647607 s in the future tar: ./usr/share/zsh/vendor-completions: time stamp 2027-02-01 12:10:16 is 33911722.150511021 s in the future tar: ./usr/share/zsh: time stamp 2027-02-01 12:10:16 is 33911722.150483678 s in the future tar: ./usr/share/libgcrypt20: time stamp 2027-02-01 12:10:23 is 33911729.150393018 s in the future tar: ./usr/share/man/fr/man7: time stamp 2027-02-01 12:10:16 is 33911722.150263386 s in the future tar: ./usr/share/man/fi/man1: time stamp 2027-02-01 12:10:53 is 33911759.1452528 s in the future tar: ./usr/share/man/id/man8: time stamp 2027-02-01 12:10:53 is 33911759.144813219 s in the future tar: ./usr/share/man/id/man1: time stamp 2027-02-01 12:10:53 is 33911759.144732738 s in the future tar: ./usr/share/man/id: time stamp 2027-02-01 12:10:53 is 33911759.144711763 s in the future tar: ./usr/share/man/uk/man8: time stamp 2027-02-01 12:10:53 is 33911759.144139517 s in the future tar: ./usr/share/man/uk/man1: time stamp 2027-02-01 12:10:53 is 33911759.14362325 s in the future tar: ./usr/share/man/uk/man5: time stamp 2027-02-01 12:10:53 is 33911759.143443963 s in the future tar: ./usr/share/man/uk: time stamp 2027-02-01 12:10:53 is 33911759.143416524 s in the future tar: ./usr/share/man/pt: time stamp 2027-02-01 12:10:07 is 33911713.139127127 s in the future tar: ./usr/share/man/nl: time stamp 2027-02-01 12:10:07 is 33911713.134485077 s in the future tar: ./usr/share/man/zh_CN/man8: time stamp 2027-02-01 12:10:53 is 33911759.133905803 s in the future tar: ./usr/share/man/zh_CN/man1: time stamp 2027-02-01 12:10:53 is 33911759.133683633 s in the future tar: ./usr/share/man/zh_CN/man5: time stamp 2027-02-01 12:10:53 is 33911759.133495371 s in the future tar: ./usr/share/man/zh_CN: time stamp 2027-02-01 12:10:53 is 33911759.133468826 s in the future tar: ./usr/share/man/tr/man8: time stamp 2027-02-01 12:10:53 is 33911759.133216473 s in the future tar: ./usr/share/man/tr/man1: time stamp 2027-02-01 12:10:53 is 33911759.133066344 s in the future tar: ./usr/share/man/tr/man5: time stamp 2027-02-01 12:10:53 is 33911759.132955045 s in the future tar: ./usr/share/man/tr: time stamp 2027-02-01 12:10:53 is 33911759.132929483 s in the future tar: ./usr/share/man/hu/man1: time stamp 2027-02-01 12:10:53 is 33911759.13276616 s in the future tar: ./usr/share/man/hu/man5: time stamp 2027-02-01 12:10:53 is 33911759.132684644 s in the future tar: ./usr/share/man/hu: time stamp 2027-02-01 12:10:53 is 33911759.132659145 s in the future tar: ./usr/share/man/sv/man7: time stamp 2027-02-01 12:10:16 is 33911722.132503171 s in the future tar: ./usr/share/man/sv/man8: time stamp 2027-02-01 12:10:53 is 33911759.132152028 s in the future tar: ./usr/share/man/sv/man5: time stamp 2027-02-01 12:10:53 is 33911759.129940275 s in the future tar: ./usr/share/man/ro/man8: time stamp 2027-02-01 12:09:42 is 33911688.128976165 s in the future tar: ./usr/share/man/ro/man1: time stamp 2027-02-01 12:10:56 is 33911762.128525962 s in the future tar: ./usr/share/man/ro: time stamp 2027-02-01 12:10:30 is 33911736.128499368 s in the future tar: ./usr/share/man/ko/man8: time stamp 2027-02-01 12:10:53 is 33911759.128373983 s in the future tar: ./usr/share/man/ko/man1: time stamp 2027-02-01 12:10:53 is 33911759.127979292 s in the future tar: ./usr/share/man/ko/man5: time stamp 2027-02-01 12:10:53 is 33911759.127892791 s in the future tar: ./usr/share/man/ko: time stamp 2027-02-01 12:10:53 is 33911759.127866846 s in the future tar: ./usr/share/man/zh_TW/man8: time stamp 2027-02-01 12:10:53 is 33911759.118008445 s in the future tar: ./usr/share/man/zh_TW/man1: time stamp 2027-02-01 12:10:53 is 33911759.117887301 s in the future tar: ./usr/share/man/zh_TW/man5: time stamp 2027-02-01 12:10:53 is 33911759.117793815 s in the future tar: ./usr/share/man/zh_TW: time stamp 2027-02-01 12:10:53 is 33911759.117768395 s in the future tar: ./usr/share/man/man3: time stamp 2027-02-01 12:10:21 is 33911727.095233557 s in the future tar: ./usr/share/man/da/man8: time stamp 2027-02-01 12:10:53 is 33911759.095026793 s in the future tar: ./usr/share/man/da/man1: time stamp 2027-02-01 12:10:53 is 33911759.094941248 s in the future tar: ./usr/share/man/da/man5: time stamp 2027-02-01 12:10:53 is 33911759.09485474 s in the future tar: ./usr/share/man/da: time stamp 2027-02-01 12:10:53 is 33911759.09482919 s in the future tar: ./usr/share/man/cs/man1: time stamp 2027-02-01 12:10:53 is 33911759.094460423 s in the future tar: ./usr/share/man/cs/man5: time stamp 2027-02-01 12:10:53 is 33911759.094322208 s in the future tar: ./usr/share/man/sl/man8: time stamp 2027-02-01 12:09:46 is 33911692.09174148 s in the future tar: ./usr/share/man/pt_BR/man8: time stamp 2027-02-01 12:10:53 is 33911759.091480521 s in the future tar: ./usr/share/man/pt_BR/man1: time stamp 2027-02-01 12:10:53 is 33911759.091134737 s in the future tar: ./usr/share/man/pt_BR/man5: time stamp 2027-02-01 12:10:53 is 33911759.09101158 s in the future tar: ./usr/share/man/pt_BR: time stamp 2027-02-01 12:10:53 is 33911759.09098471 s in the future tar: ./usr/share/man/ru/man8: time stamp 2027-02-01 12:10:54 is 33911760.090208705 s in the future tar: ./usr/share/man/ru/man1: time stamp 2027-02-01 12:10:54 is 33911760.089910942 s in the future tar: ./usr/share/man/ru/man5: time stamp 2027-02-01 12:10:53 is 33911759.089736032 s in the future tar: ./usr/share/man/ru: time stamp 2027-02-01 12:10:53 is 33911759.089709899 s in the future tar: ./usr/share/util-linux/logcheck/ignore.d.server: time stamp 2027-02-01 12:09:59 is 33911705.089578653 s in the future tar: ./usr/share/keyrings: time stamp 2027-02-01 12:10:15 is 33911721.088404734 s in the future tar: ./usr/share/tabset: time stamp 2027-02-01 12:09:57 is 33911703.088176181 s in the future tar: ./usr/share/polkit-1/actions: time stamp 2027-02-01 12:09:49 is 33911695.08804002 s in the future tar: ./usr/share/pam: time stamp 2027-02-01 12:09:54 is 33911700.087627018 s in the future tar: ./usr/share/debianutils/shells.d: time stamp 2027-02-01 12:09:44 is 33911690.087438596 s in the future tar: ./usr/share/debianutils: time stamp 2027-02-01 12:09:46 is 33911692.087412703 s in the future tar: ./usr/share/menu: time stamp 2027-02-01 12:10:55 is 33911761.085837959 s in the future tar: ./usr/share/lintian/profiles/dpkg: time stamp 2027-02-01 12:09:49 is 33911695.083721849 s in the future tar: ./usr/share/lintian: time stamp 2027-02-01 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33911683.578178933 s in the future tar: ./usr/share/locale/de: time stamp 2027-02-01 12:09:28 is 33911667.578160566 s in the future tar: ./usr/share/locale/ko/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.578141055 s in the future tar: ./usr/share/locale/ko: time stamp 2027-02-01 12:09:28 is 33911667.578123083 s in the future tar: ./usr/share/locale/ro/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.578102947 s in the future tar: ./usr/share/locale/ro: time stamp 2027-02-01 12:09:28 is 33911667.578084437 s in the future tar: ./usr/share/locale/lt/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.578064526 s in the future tar: ./usr/share/locale/lt: time stamp 2027-02-01 12:09:28 is 33911667.578045976 s in the future tar: ./usr/share/locale/es/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.578026084 s in the future tar: ./usr/share/locale/es: time stamp 2027-02-01 12:09:28 is 33911667.578007467 s in the future tar: ./usr/share/locale/be/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.577987719 s in the future tar: ./usr/share/locale/sv/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.577948475 s in the future tar: ./usr/share/locale/sv: time stamp 2027-02-01 12:09:28 is 33911667.577929204 s in the future tar: ./usr/share/locale/hu/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.577908939 s in the future tar: ./usr/share/locale/hu: time stamp 2027-02-01 12:09:28 is 33911667.577890534 s in the future tar: ./usr/share/locale/tr/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.577870081 s in the future tar: ./usr/share/locale/tr: time stamp 2027-02-01 12:09:28 is 33911667.577851769 s in the future tar: ./usr/share/locale/nb/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.577831758 s in the future tar: ./usr/share/locale/nb: time stamp 2027-02-01 12:09:28 is 33911667.573600794 s in the future tar: ./usr/share/locale/et/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573547482 s in the future tar: ./usr/share/locale/et: time stamp 2027-02-01 12:09:28 is 33911667.573504055 s in the future tar: ./usr/share/locale/zh_CN/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573466736 s in the future tar: ./usr/share/locale/zh_CN: time stamp 2027-02-01 12:09:28 is 33911667.573426942 s in the future tar: ./usr/share/locale/nl/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573389471 s in the future tar: ./usr/share/locale/nl: time stamp 2027-02-01 12:09:28 is 33911667.573349731 s in the future tar: ./usr/share/locale/sr/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573312895 s in the future tar: ./usr/share/locale/sr: time stamp 2027-02-01 12:09:28 is 33911667.573273024 s in the future tar: ./usr/share/locale/pt/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573235847 s in the future tar: ./usr/share/locale/pt: time stamp 2027-02-01 12:09:28 is 33911667.573195502 s in the future tar: ./usr/share/locale/uk/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573154627 s in the future tar: ./usr/share/locale/uk: time stamp 2027-02-01 12:09:28 is 33911667.573119818 s in the future tar: ./usr/share/locale/id/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.573079374 s in the future tar: ./usr/share/locale/id: time stamp 2027-02-01 12:09:28 is 33911667.573041779 s in the future tar: ./usr/share/locale/fi/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.572999512 s in the future tar: ./usr/share/locale/fi: time stamp 2027-02-01 12:09:28 is 33911667.572964643 s in the future tar: ./usr/share/locale/fr/LC_TIME: time stamp 2027-02-01 12:09:44 is 33911683.57292178 s in the future tar: ./usr/share/locale/fr: time stamp 2027-02-01 12:09:28 is 33911667.572882999 s in the future tar: ./usr/share/locale: time stamp 2027-02-01 12:10:54 is 33911753.572849963 s in the future tar: ./usr/share/man/sl/man1: time stamp 2027-02-01 12:10:00 is 33911699.572806149 s in the future tar: ./usr/share/man/cs/man8: time stamp 2027-02-01 12:11:21 is 33911780.572744083 s in the future tar: ./usr/share/man/cs: time stamp 2027-02-01 12:10:53 is 33911752.572707602 s in the future tar: ./usr/share/man/it/man1: time stamp 2027-02-01 12:10:54 is 33911753.572682744 s in the future tar: ./usr/share/man/it: time stamp 2027-02-01 12:09:28 is 33911667.572648579 s in the future tar: ./usr/share/man/ja/man1: time stamp 2027-02-01 12:10:53 is 33911752.572628314 s in the future tar: ./usr/share/man/ja: time stamp 2027-02-01 12:09:28 is 33911667.572593262 s in the future tar: ./usr/share/man/gl/man8: time stamp 2027-02-01 12:11:21 is 33911780.572573757 s in the future tar: ./usr/share/man/gl: time stamp 2027-02-01 12:10:54 is 33911753.57255529 s in the future tar: ./usr/share/man/pl/man1: time stamp 2027-02-01 12:10:53 is 33911752.572535161 s in the future tar: ./usr/share/man/pl: time stamp 2027-02-01 12:09:28 is 33911667.572500653 s in the future tar: ./usr/share/man/de: time stamp 2027-02-01 12:10:07 is 33911706.572417645 s in the future tar: ./usr/share/man/es/man1: time stamp 2027-02-01 12:11:20 is 33911779.572396624 s in the future tar: ./usr/share/man/es: time stamp 2027-02-01 12:09:28 is 33911667.572361696 s in the future tar: ./usr/share/man/sv/man1: time stamp 2027-02-01 12:11:20 is 33911779.572341425 s in the future tar: ./usr/share/man/sv: time stamp 2027-02-01 12:10:16 is 33911715.57232126 s in the future tar: ./usr/share/man/fi/man8: time stamp 2027-02-01 12:11:21 is 33911780.572285381 s in the future tar: ./usr/share/man/fi: time stamp 2027-02-01 12:10:54 is 33911753.572243066 s in the future tar: ./usr/share/man/fr: time stamp 2027-02-01 12:10:15 is 33911714.572158712 s in the future tar: ./usr/share/man: time stamp 2027-02-01 12:10:54 is 33911753.572115052 s in the future tar: ./usr/share: time stamp 2027-02-01 12:10:55 is 33911754.572078703 s in the future tar: ./usr: time stamp 2027-02-01 12:09:32 is 33911671.572039613 s in the future tar: ./etc/systemd/system/timers.target.wants: time stamp 2027-02-01 12:10:36 is 33911735.571978453 s in the future tar: ./etc/systemd/system: time stamp 2027-02-01 12:09:33 is 33911672.571937407 s in the future tar: ./etc/alternatives: time stamp 2027-02-01 12:11:21 is 33911780.571873149 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gubbins_3.4-1.dsc] I: copying [./gubbins_3.4.orig.tar.gz] I: copying [./gubbins_3.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 30 18:13:39 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gubbins_3.4-1.dsc: no acceptable signature found dpkg-source: info: extracting gubbins in gubbins-3.4 dpkg-source: info: unpacking gubbins_3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_3.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying iqtree2.patch dpkg-source: info: applying autoupdate_configure.ac.patch dpkg-source: info: applying python3-shebang.patch dpkg-source: info: applying remove-numba-temporarily.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1064781/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='733748f036d9454397a4b404f06d33f7' 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='1064781' PS1='# ' PS2='> ' 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.11U7qGOk/pbuilderrc_CCHb --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/b1 --logfile b1/build.log gubbins_3.4-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1064781/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, autoconf-archive, pkgconf, fasttree, iqtree, raxml, python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, tox, python3-scipy, python3-multiprocess, python3-wheel dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19962 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on iqtree; however: Package iqtree is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on tox; however: Package tox is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-wheel; however: Package python3-wheel is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} iqtree{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-plugins{a} libhwloc15{a} libibmad5{a} libibumad3{a} libibverbs1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnl-3-200{a} libnl-route-3-200{a} libnsl2{a} libnuma1{a} libopenjp2-7{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix2t64{a} libpng16-16t64{a} libpsm-infinipath1{a} libpsm2-2{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} librdmacm1t64{a} libreadline8t64{a} libsharpyuv0{a} libsubunit-dev{a} libsubunit0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libucx0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} ocl-icd-libopencl1{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-biopython{a} python3-cachetools{a} python3-cairo{a} python3-chardet{a} python3-colorama{a} python3-decorator{a} python3-dendropy{a} python3-dill{a} python3-distlib{a} python3-filelock{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pip-whl{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-pyproject-api{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-whl{a} python3-typeguard{a} python3-typing-extensions{a} python3-virtualenv{a} python3-wheel{a} python3-wheel-whl{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} raxml{a} readline-common{a} sensible-utils{a} sgml-base{a} tox{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-dev python3-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 184 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB of archives. After unpacking 663 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libsubunit0 amd64 1.4.2-3+b1 [6436 B] Get: 43 http://deb.debian.org/debian trixie/main amd64 libsubunit-dev amd64 1.4.2-3+b1 [7352 B] Get: 44 http://deb.debian.org/debian trixie/main amd64 check amd64 0.15.2-2+b1 [113 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fasttree amd64 2.1.11-2 [181 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 81 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.4-1 [661 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 111 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-3 [510 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 iqtree amd64 2.0.7+dfsg-1+b1 [3671 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.84+dfsg-4+b1 [1651 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-cachetools all 5.3.3-1 [13.2 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-dendropy all 4.6.1-2 [277 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-dill all 0.3.9-1 [83.5 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-distlib all 0.3.9-1 [257 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-filelock all 3.16.1-1 [12.6 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-multiprocess all 0.70.17-1 [107 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-pip-whl all 24.3.1+dfsg-1 [1501 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-api all 1.8.0-1 [51.7 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-setuptools-whl all 74.1.2-2 [1262 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-wheel-whl all 0.45.1-1 [75.3 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-virtualenv all 20.28.0+ds-1 [71.3 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 raxml amd64 8.2.13+dfsg-1+b1 [1499 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 tox all 4.23.0-1 [393 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 157 MB in 3s (46.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package autoconf-archive. (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 ... 19962 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. 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Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 5 12:15:37 UTC 2026. Universal Time is now: Mon Jan 5 12:15:37 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libfontenc1:amd64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libmunge2:amd64 (0.5.15-4+b1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gubbins-3.4/ && 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 > ../gubbins_3.4-1_source.changes dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 3.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete rm -rf python/output_alignment python/tmp* tests/.deps make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:29: installing './compile' configure.ac:14: installing './config.guess' configure.ac:14: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking how to create a pax tar archive... gnutar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... 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(cached) none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether to build with code coverage support... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking for zlib.h... yes checking for math.h... yes checking for a Python interpreter with version >= 3.8... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.12 checking for python3 platform... linux checking for GNU default python3 prefix... ${prefix} checking for GNU default python3 exec_prefix... ${exec_prefix} checking for python3 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.12/site-packages checking for python3 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.12/site-packages checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' make all-recursive make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making all in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o Newickform.lo Newickform.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alignment_file.lo alignment_file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o block_tab_file.lo block_tab_file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o branch_sequences.lo branch_sequences.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o string_cat.lo string_cat.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o fasta_of_snp_sites.lo fasta_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 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-I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parse_vcf.lo parse_vcf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o phylip_of_snp_sites.lo phylip_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o seqUtil.lo seqUtil.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_searching.lo snp_searching.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o snp_sites.lo snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_statistics.lo tree_statistics.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o tree_scaling.lo tree_scaling.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o vcf.lo vcf.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o csv_of_snp_sites.lo csv_of_snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -fPIC -DPIC -o .libs/branch_sequences.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -fPIC -DPIC -o .libs/phylip_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -fPIC -DPIC -o .libs/seqUtil.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -fPIC -DPIC -o .libs/tree_statistics.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -fPIC -DPIC -o .libs/string_cat.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -fPIC -DPIC -o .libs/gubbins.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -fPIC -DPIC -o .libs/snp_searching.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -fPIC -DPIC -o .libs/parse_phylip.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -fPIC -DPIC -o .libs/parse_vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -fPIC -DPIC -o .libs/csv_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c phylip_of_snp_sites.c -o phylip_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c csv_of_snp_sites.c -o csv_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c gubbins.c -o gubbins.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_sites.c -o snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c vcf.c -o vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_vcf.c -o parse_vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c snp_searching.c -o snp_searching.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c alignment_file.c -o alignment_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c Newickform.c -o Newickform.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c parse_phylip.c -o parse_phylip.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c branch_sequences.c -o branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -version-info 0:1 -Wl,-z,relro -Wl,-z,now -pthread -o libgubbins.la -rpath /usr/lib/x86_64-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo csv_of_snp_sites.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o .libs/csv_of_snp_sites.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cr .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o csv_of_snp_sites.o libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm -pthread make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making all in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' # make sure test data will not be changed (at least tests/data/multiple_recombinations.tre is removed in the test) cp -a tests/data tests/data.save dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making check in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make run_all_tests make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 27 | fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -pthread -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests --coverage -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gubbins-3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make check-TESTS make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[5]: Entering directory '/build/reproducible-path/gubbins-3.4/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins package_version ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making check in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' rm -rf tests/data mv tests/data.save tests/data make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/gubbins-3.4/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gubbins-3.4' Making install in src make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/src' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/src' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: install: ranlib /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/reproducible-path/gubbins-3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/src' Making install in release make[3]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4/release' make[3]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Entering directory '/build/reproducible-path/gubbins-3.4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[3]: Leaving directory '/build/reproducible-path/gubbins-3.4' make[2]: Leaving directory '/build/reproducible-path/gubbins-3.4' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating build creating build/lib creating build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins copying gubbins/utils.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/treebuilders.py -> build/lib/gubbins copying gubbins/run_gubbins.py -> build/lib/gubbins copying gubbins/pyjar.py -> build/lib/gubbins creating build/lib/gubbins/tests copying gubbins/tests/test_python_scripts.py -> build/lib/gubbins/tests copying gubbins/tests/test_tree_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_alignment_python_methods.py -> build/lib/gubbins/tests copying gubbins/tests/test_pre_process_fasta.py -> build/lib/gubbins/tests copying gubbins/tests/test_converging_recombinations.py -> build/lib/gubbins/tests copying gubbins/tests/__init__.py -> build/lib/gubbins/tests copying gubbins/tests/test_utils.py -> build/lib/gubbins/tests copying gubbins/tests/test_dependencies.py -> build/lib/gubbins/tests copying gubbins/tests/test_treebuilders.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_starting_tree.py -> build/lib/gubbins/tests copying gubbins/tests/test_validate_fasta_input.py -> build/lib/gubbins/tests running build_scripts creating build/scripts-3.12 copying and adjusting scripts/generate_ska_alignment.py -> build/scripts-3.12 copying and adjusting scripts/extract_gubbins_clade.py -> build/scripts-3.12 copying and adjusting scripts/mask_gubbins_aln.py -> build/scripts-3.12 copying and adjusting scripts/gubbins_alignment_checker.py -> build/scripts-3.12 copying and adjusting scripts/generate_files_for_clade_analysis.py -> build/scripts-3.12 copying and adjusting scripts/count_recombinations_per_gene.py -> build/scripts-3.12 copying and adjusting scripts/extract_recombinant_sequences.py -> build/scripts-3.12 copying ../R/scripts/plot_gubbins.R -> build/scripts-3.12 changing mode of build/scripts-3.12/generate_ska_alignment.py from 644 to 755 changing mode of build/scripts-3.12/extract_gubbins_clade.py from 644 to 755 changing mode of build/scripts-3.12/mask_gubbins_aln.py from 644 to 755 changing mode of build/scripts-3.12/gubbins_alignment_checker.py from 644 to 755 changing mode of build/scripts-3.12/generate_files_for_clade_analysis.py from 644 to 755 changing mode of build/scripts-3.12/count_recombinations_per_gene.py from 644 to 755 changing mode of build/scripts-3.12/extract_recombinant_sequences.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_python_scripts.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_tree_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_alignment_python_methods.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_pre_process_fasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_converging_recombinations.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_dependencies.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_starting_tree.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/tests/test_validate_fasta_input.py -> ../debian/gubbins/usr/share/gubbins/gubbins/tests copying build/lib/gubbins/utils.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/treebuilders.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/pyjar.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_python_scripts.py to test_python_scripts.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_tree_methods.py to test_tree_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_alignment_python_methods.py to test_alignment_python_methods.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_pre_process_fasta.py to test_pre_process_fasta.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_converging_recombinations.py to test_converging_recombinations.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_utils.py to test_utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_dependencies.py to test_dependencies.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_treebuilders.py to test_treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_starting_tree.py to test_validate_starting_tree.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/tests/test_validate_fasta_input.py to test_validate_fasta_input.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/utils.py to utils.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/treebuilders.py to treebuilders.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/run_gubbins.py to run_gubbins.cpython-312.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/pyjar.py to pyjar.cpython-312.pyc running install_egg_info running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing entry points to gubbins.egg-info/entry_points.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' adding license file 'LICENSE.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-3.4.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/generate_ska_alignment.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/extract_gubbins_clade.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/extract_recombinant_sequences.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/count_recombinations_per_gene.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/generate_files_for_clade_analysis.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/mask_gubbins_aln.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/gubbins_alignment_checker.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.12/plot_gubbins.R -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/generate_ska_alignment.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_gubbins_clade.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/extract_recombinant_sequences.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/count_recombinations_per_gene.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/generate_files_for_clade_analysis.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/mask_gubbins_aln.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_alignment_checker.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/plot_gubbins.R to 755 Installing run_gubbins.py script to ../debian/gubbins/usr/share/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/gubbins-3.4' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/reproducible-path/gubbins-3.4' dh_installdocs dh_installchangelogs dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1: DWARF compression not beneficial - old size 77557 new size 78812 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/x86_64-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins' in '../gubbins_3.4-1_amd64.deb'. dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_3.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gubbins_3.4-1_amd64.buildinfo dpkg-genchanges --build=binary -O../gubbins_3.4-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/1064781 and its subdirectories I: Current time: Mon Jan 5 00:17:03 -12 2026 I: pbuilder-time-stamp: 1767615423 Tue Dec 3 05:54:04 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Dec 3 05:54:04 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Dec 3 06:09:15 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Dec 3 06:09:16 UTC 2024 I: gubbins_3.4-1_amd64.changes: Format: 1.8 Date: Sat, 30 Nov 2024 19:00:21 +0100 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: amd64 Version: 3.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gubbins - phylogenetic analysis of genome sequences Changes: gubbins (3.4-1) unstable; urgency=medium . * New upstream version 3.4 * d/copyright: document missing copyright owners. Those are Wellcome Trust Sanger Institute and Imperial College London. * d/control: declare compliance to standards version 4.7.0. * d/patches/*: normalise last-update timestamp to dep3. Checksums-Sha1: 176c23f4e7fa4c760cfc49c41c026d540c9eb076 84408 gubbins-dbgsym_3.4-1_amd64.deb b931735effc631e6fac65ce14d97f877abdf03db 9942 gubbins_3.4-1_amd64.buildinfo cd47e40c81e859feed0ee2f5fc25ca0f707987a1 95024 gubbins_3.4-1_amd64.deb Checksums-Sha256: 7f3f64b3862157a769866f6f2b796a2c22f803d66926d34c2fa70892c4756ca6 84408 gubbins-dbgsym_3.4-1_amd64.deb e06bea4d832a63a95b09b9b9d920a5e55072d8db0a2bb47c796817d371187c77 9942 gubbins_3.4-1_amd64.buildinfo b9e7ab8ef5d92546b17a0d0c8a63ceb0103392aa4a8f66adbb0e61d35ef0675d 95024 gubbins_3.4-1_amd64.deb Files: b1a11ebb8c5468a1ee38bf123518379c 84408 debug optional gubbins-dbgsym_3.4-1_amd64.deb 182a01e618247871dd242f25c119d640 9942 science optional gubbins_3.4-1_amd64.buildinfo a6fdf7f5d22d5f78ec9f1a1b0a90822f 95024 science optional gubbins_3.4-1_amd64.deb Tue Dec 3 06:09:17 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_8-41258.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/gubbins_3.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/gubbins_3.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/gubbins_3.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/b1/gubbins_3.4-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.11U7qGOk/b2/gubbins_3.4-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.350s) 0.350s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.017s) 0.017s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 676ms CPU time consumed: 676ms Tue Dec 3 06:09:18 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 3 06:09:18 UTC 2024 I: gubbins from trixie built successfully and reproducibly on amd64. Tue Dec 3 06:09:20 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 3 06:09:20 UTC 2024 I: Submitting 12K b1/gubbins_3.4-1_amd64.buildinfo.asc Tue Dec 3 06:09:22 UTC 2024 I: Submitting 12K b2/gubbins_3.4-1_amd64.buildinfo.asc Tue Dec 3 06:09:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 3 06:09:25 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 3 06:09:25 UTC 2024 I: Removing signed gubbins_3.4-1_amd64.buildinfo.asc files: removed './b1/gubbins_3.4-1_amd64.buildinfo.asc' removed './b2/gubbins_3.4-1_amd64.buildinfo.asc'