Wed Apr 26 23:39:07 UTC 2023 I: starting to build jellyfish/bookworm/arm64 on jenkins on '2023-04-26 23:38' Wed Apr 26 23:39:07 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/26556/console.log Wed Apr 26 23:39:07 UTC 2023 I: Downloading source for bookworm/jellyfish=2.3.0-15 --2023-04-26 23:39:07-- http://cdn-fastly.deb.debian.org/debian/pool/main/j/jellyfish/jellyfish_2.3.0-15.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3224 (3.1K) [text/prs.lines.tag] Saving to: ‘jellyfish_2.3.0-15.dsc’ 0K ... 100% 338M=0s 2023-04-26 23:39:07 (338 MB/s) - ‘jellyfish_2.3.0-15.dsc’ saved [3224/3224] Wed Apr 26 23:39:07 UTC 2023 I: jellyfish_2.3.0-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: jellyfish Binary: jellyfish, libjellyfish-2.0-2, libjellyfish-2.0-dev, python3-dna-jellyfish, libjellyfish-perl, jellyfish-examples Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386 ia64 kfreebsd-amd64 kfreebsd-i386 riscv64 all Version: 2.3.0-15 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/gmarcais/Jellyfish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), d-shlibs, autoconf-archive, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools Package-List: jellyfish deb science optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 jellyfish-examples deb science optional arch=all libjellyfish-2.0-2 deb libs optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 libjellyfish-2.0-dev deb libdevel optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 libjellyfish-perl deb perl optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 python3-dna-jellyfish deb python optional arch=amd64,arm64,armel,armhf,i386,mips64el,ppc64el,hppa,hurd-i386,ia64,kfreebsd-amd64,kfreebsd-i386,riscv64 Checksums-Sha1: 4f7f5263e6e097c623531a660ef6158e2fb5e17b 679125 jellyfish_2.3.0.orig.tar.gz dcb7d3cd40572c6cabf719addd384aa9c2f34c5d 15376 jellyfish_2.3.0-15.debian.tar.xz Checksums-Sha256: 29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz 9c3b7bccfa8ba49078452b8bd6534295cfa1eb84bd4ab0c5b395b93fae8f8d7c 15376 jellyfish_2.3.0-15.debian.tar.xz Files: b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz 0869f7bc0fe3da61452888ad0c293dd3 15376 jellyfish_2.3.0-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM0qaIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGyvQ/+LdIqzPAjO0e/0FqrTNDOVcY88Cd5DTbX 4wRqju3HjroPvndTTdgWVdafoABGz5zL/FyGKQ4if4mXxb37jE1GVplFc02+8EWw elLo0JwTV8J7yMPQhEn+tRTaPlhhtl+SQWbduWhcTcO8675iPYL2pjcE6nTxRarq PntLh/oagekRyd23SFYrYWd1bzhlU5gil51+IGUG/pym0KYq27xKgb4ZjfIC1gS6 uQE9SQ78KbJFFpfbtyQ0HimBSM/3vS81L97PruBVzaZ+BnchpzD4qx4O5Q7aMlPQ hUh1OpREe1HxVfEcho3ZIf8si2F2v5+Cs1gt1891ZDh84v0rKBZeNa07KsmHKuQr 1d5wBY2NUZj3QIfqGHUXMWevjriPQmGFzyM/CvFOHNptcaeyJdcn3TjSABIXi1gv AskBrxJhDS1CVHw6UoQ5l2X0dKDR7yk0fSqgrtbuqR3mhPncb391VU8h1MkuSKWb z8Wh2mlyNzYNskNugavoeG1JWaQbdzkGL4shj+Z8AVkJ9psgfpwW8EMELrtzjIzY Ap6qu2btDY2dO1j/joKRq7WI+Op1R5KymfciGewZwn7lQx+ATGEY1qG6VJ/ENbix hyi6iilENjoFs9rlBHNlGWURcknT40fFVKbV0tIIw741sYAIWKoK6z8LwRqmpbZ7 ud1Ks+TMSjA= =XmJN -----END PGP SIGNATURE----- Wed Apr 26 23:39:07 UTC 2023 I: Checking whether the package is not for us Wed Apr 26 23:39:07 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Wed Apr 26 23:39:07 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Wed Apr 26 23:55:04 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 26 11:39:11 -12 2023 I: pbuilder-time-stamp: 1682552351 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] tar: ./bin: time stamp 2024-05-28 04:48:56 is 34362584.57173798 s in the future tar: ./dev/shm: time stamp 2024-05-28 16:30:22 is 34404670.57153124 s in the future tar: ./dev/null: time stamp 2024-05-28 04:48:25 is 34362553.57140082 s in the future tar: ./dev/zero: time stamp 2024-05-28 04:48:25 is 34362553.57135068 s in the future tar: ./dev/full: time stamp 2024-05-28 04:48:25 is 34362553.57131056 s in the future tar: ./dev/random: time stamp 2024-05-28 04:48:25 is 34362553.57127334 s in the future tar: ./dev/urandom: time stamp 2024-05-28 04:48:25 is 34362553.57123724 s in the future tar: ./dev/tty: time stamp 2024-05-28 04:48:25 is 34362553.57120134 s in the future tar: ./dev/console: time stamp 2024-05-28 04:48:25 is 34362553.57116588 s in the future tar: ./dev/pts: time stamp 2024-05-28 04:48:25 is 34362553.57112514 s in the future tar: ./dev/ptmx: time stamp 2024-05-28 04:48:25 is 34362553.57109354 s in the future tar: ./etc/resolv.conf: time stamp 2024-05-28 16:30:22 is 34404670.57101202 s in the future tar: ./etc/mailname: time stamp 2024-05-28 16:30:22 is 34404670.57095186 s in the future tar: ./etc/hostname: time stamp 2024-05-28 16:30:22 is 34404670.57090714 s in the future tar: ./etc/hosts: time stamp 2024-05-28 16:30:22 is 34404670.57086654 s in the future tar: ./etc/apt/sources.list: time stamp 2024-05-28 04:50:35 is 34362683.57074606 s in the future tar: ./etc/apt/apt.conf.d/80proxy: time stamp 2024-05-28 04:50:35 is 34362683.57069136 s in the future tar: ./etc/apt/apt.conf.d: time stamp 2024-05-28 04:50:35 is 34362683.57056244 s in the future tar: ./etc/apt/trusted.gpg.d: time stamp 2024-05-28 04:48:47 is 34362575.56988776 s in the future tar: ./etc/apt: time stamp 2024-05-28 04:50:35 is 34362683.56984696 s in the future tar: ./etc/default: time stamp 2024-05-28 04:48:54 is 34362582.56926316 s in the future tar: ./etc/dpkg/origins/default: time stamp 2024-05-28 04:48:26 is 34362554.56915336 s in the future tar: ./etc/dpkg/origins: time stamp 2024-05-28 04:48:49 is 34362577.56912032 s in the future tar: ./etc/dpkg/dpkg.cfg.d/02speedup: time stamp 2024-05-28 04:50:35 is 34362683.56903098 s in the future tar: ./etc/dpkg/dpkg.cfg.d: time stamp 2024-05-28 04:50:35 is 34362683.5689959 s in the future tar: ./etc/skel: time stamp 2024-05-28 04:48:49 is 34362577.56867034 s in the future tar: ./etc/update-motd.d: time stamp 2024-05-28 04:48:49 is 34362577.56859156 s in the future tar: ./etc/cron.d: time stamp 2024-05-28 04:48:49 is 34362577.56729454 s in the future tar: ./etc/selinux: time stamp 2024-05-28 04:48:47 is 34362575.5665201 s in the future tar: ./etc/terminfo: time stamp 2024-05-28 04:48:48 is 34362576.5664329 s in the future tar: ./etc/security/opasswd: time stamp 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the future tar: ./etc/opt: time stamp 2024-05-28 04:48:26 is 34362554.56487112 s in the future tar: ./etc/timezone: time stamp 2024-05-28 04:48:48 is 34362576.56482748 s in the future tar: ./etc/environment: time stamp 2024-05-28 04:48:54 is 34362582.564749 s in the future tar: ./etc/.pwd.lock: time stamp 2024-05-28 04:48:54 is 34362582.56471048 s in the future tar: ./etc/shadow: time stamp 2024-05-28 04:48:54 is 34362582.5646061 s in the future tar: ./etc/passwd-: time stamp 2024-05-28 04:48:25 is 34362553.56451038 s in the future tar: ./etc/passwd: time stamp 2024-05-28 04:48:54 is 34362582.56445574 s in the future tar: ./etc/gshadow: time stamp 2024-05-28 04:48:54 is 34362582.56436652 s in the future tar: ./etc/group-: time stamp 2024-05-28 04:48:25 is 34362553.56429082 s in the future tar: ./etc/group: time stamp 2024-05-28 04:48:54 is 34362582.56424382 s in the future tar: ./etc/subuid: time stamp 2024-05-28 04:48:54 is 34362582.56420748 s in the future tar: ./etc/subgid: time stamp 2024-05-28 04:48:54 is 34362582.56417234 s in the future tar: ./etc/shells: time stamp 2024-05-28 04:48:56 is 34362584.56413058 s in the future tar: ./lib: time stamp 2024-05-28 04:48:56 is 34362584.5638139 s in the future tar: ./media: time stamp 2024-05-28 04:48:26 is 34362554.56375884 s in the future tar: ./mnt: time stamp 2024-05-28 04:48:26 is 34362554.56371942 s in the future tar: ./opt: time stamp 2024-05-28 04:48:26 is 34362554.56368464 s in the future tar: ./root: time stamp 2024-05-28 04:48:26 is 34362554.5635586 s in the future tar: ./run/mount: time stamp 2024-05-28 04:48:25 is 34362553.56348718 s in the future tar: ./run/lock: time stamp 2024-05-28 04:48:26 is 34362554.56344914 s in the future tar: ./sbin: time stamp 2024-05-28 04:48:56 is 34362584.56341642 s in the future tar: ./srv: time stamp 2024-05-28 04:48:26 is 34362554.56337962 s in the future tar: ./tmp: time stamp 2024-05-28 16:30:31 is 34404679.56332674 s in the future tar: ./usr/lib/aarch64-linux-gnu/e2fsprogs: time stamp 2024-05-28 04:48:35 is 34362563.56295686 s in the future tar: ./usr/lib/aarch64-linux-gnu/gconv/gconv-modules.d: time stamp 2024-05-28 04:48:37 is 34362565.56276374 s in the future tar: ./usr/lib/aarch64-linux-gnu/gconv: time stamp 2024-05-28 04:48:37 is 34362565.37040066 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/B: time stamp 2024-05-28 04:48:42 is 34362570.36919502 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/CORE: time stamp 2024-05-28 04:48:42 is 34362570.3017443 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Compress/Raw: time stamp 2024-05-28 04:48:42 is 34362570.3013017 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Data: time stamp 2024-05-28 04:48:42 is 34362570.3005024 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Devel: time stamp 2024-05-28 04:48:42 is 34362570.29363944 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Digest: time stamp 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2024-05-28 04:48:42 is 34362570.29055444 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/File: time stamp 2024-05-28 04:48:42 is 34362570.2901526 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Filter/Util: time stamp 2024-05-28 04:48:42 is 34362570.29000922 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Hash/Util: time stamp 2024-05-28 04:48:42 is 34362570.28975142 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Hash: time stamp 2024-05-28 04:48:42 is 34362570.28932606 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/I18N: time stamp 2024-05-28 04:48:42 is 34362570.28920938 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/IO/Socket: time stamp 2024-05-28 04:48:42 is 34362570.28888926 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/IO: time stamp 2024-05-28 04:48:42 is 34362570.28812822 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/IPC: time stamp 2024-05-28 04:48:42 is 34362570.28770844 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/List/Util: time stamp 2024-05-28 04:48:42 is 34362570.28758946 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/List: time stamp 2024-05-28 04:48:42 is 34362570.28743186 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/MIME: time stamp 2024-05-28 04:48:42 is 34362570.28704484 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Math/BigInt: time stamp 2024-05-28 04:48:42 is 34362570.28690236 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/PerlIO: time stamp 2024-05-28 04:48:42 is 34362570.28667978 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Scalar: time stamp 2024-05-28 04:48:42 is 34362570.2865561 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Sub: time stamp 2024-05-28 04:48:42 is 34362570.28644356 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Sys: time stamp 2024-05-28 04:48:42 is 34362570.28617366 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Time: time stamp 2024-05-28 04:48:42 is 34362570.2852744 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Unicode/Collate: time stamp 2024-05-28 04:48:42 is 34362570.2849052 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Unicode: time stamp 2024-05-28 04:48:42 is 34362570.2839006 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/asm: time stamp 2024-05-28 04:48:42 is 34362570.2834171 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/asm-generic: time stamp 2024-05-28 04:48:42 is 34362570.28286146 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/B: time stamp 2024-05-28 04:48:42 is 34362570.2813445 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Compress/Raw/Bzip2: time stamp 2024-05-28 04:48:42 is 34362570.28075942 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Compress/Raw/Zlib: time stamp 2024-05-28 04:48:42 is 34362570.2799539 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Cwd: time stamp 2024-05-28 04:48:42 is 34362570.27934738 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/DB_File: time stamp 2024-05-28 04:48:42 is 34362570.27857236 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Data/Dumper: time stamp 2024-05-28 04:48:42 is 34362570.27783784 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Devel/Peek: time stamp 2024-05-28 04:48:42 is 34362570.2772917 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Digest/MD5: time stamp 2024-05-28 04:48:42 is 34362570.27620032 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Digest/SHA: time stamp 2024-05-28 04:48:42 is 34362570.27592372 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Encode/Byte: time stamp 2024-05-28 04:48:42 is 34362570.27196404 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/auto/Encode/CN: time stamp 2024-05-28 04:48:42 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./etc/rcS.d/S01hwclock.sh: time stamp 2024-05-28 04:48:49 is 34362568.54535876 s in the future tar: ./etc/rc6.d/K01hwclock.sh: time stamp 2024-05-28 04:48:49 is 34362568.54531752 s in the future tar: ./etc/rc0.d/K01hwclock.sh: time stamp 2024-05-28 04:48:49 is 34362568.54527592 s in the future tar: ./etc/localtime: time stamp 2024-05-28 04:48:48 is 34362567.54355426 s in the future tar: ./dev/fd: time stamp 2024-05-28 04:48:25 is 34362544.54347318 s in the future tar: ./dev/stdin: time stamp 2024-05-28 04:48:25 is 34362544.54343308 s in the future tar: ./dev/stdout: time stamp 2024-05-28 04:48:25 is 34362544.54339288 s in the future tar: ./dev/stderr: time stamp 2024-05-28 04:48:25 is 34362544.54335534 s in the future tar: ./var/spool: time stamp 2024-05-28 04:48:26 is 34362545.54332752 s in the future tar: ./var: time stamp 2024-05-28 04:48:26 is 34362545.54329908 s in the future tar: ./usr/share/zoneinfo/right/US: time stamp 2024-05-28 04:48:45 is 34362564.54322952 s in the future tar: ./usr/share/zoneinfo/right/Mexico: time stamp 2024-05-28 04:48:45 is 34362564.54319908 s in the future tar: ./usr/share/zoneinfo/right/Europe: time stamp 2024-05-28 04:48:45 is 34362564.54316788 s in the future tar: ./usr/share/zoneinfo/right/Chile: time stamp 2024-05-28 04:48:45 is 34362564.54313752 s in the future tar: ./usr/share/zoneinfo/right/Canada: time stamp 2024-05-28 04:48:45 is 34362564.54310678 s in the future tar: ./usr/share/zoneinfo/right/Brazil: time stamp 2024-05-28 04:48:45 is 34362564.54307632 s in the future tar: ./usr/share/zoneinfo/right/Asia: time stamp 2024-05-28 04:48:45 is 34362564.5430462 s in the future tar: ./usr/share/zoneinfo/right/Arctic: time stamp 2024-05-28 04:48:45 is 34362564.54301664 s in the future tar: ./usr/share/zoneinfo/right/Antarctica: time stamp 2024-05-28 04:48:45 is 34362564.54298618 s in the future tar: ./usr/share/zoneinfo/right: time stamp 2024-05-28 04:48:45 is 34362564.54295692 s in the future tar: ./usr/share/zoneinfo/posix: time stamp 2024-05-28 04:48:45 is 34362564.54292794 s in the future tar: ./usr/share/zoneinfo/US: time stamp 2024-05-28 04:48:45 is 34362564.54289956 s in the future tar: ./usr/share/zoneinfo/Mexico: time stamp 2024-05-28 04:48:45 is 34362564.542871 s in the future tar: ./usr/share/zoneinfo/Europe: time stamp 2024-05-28 04:48:45 is 34362564.5428413 s in the future tar: ./usr/share/zoneinfo/Chile: time stamp 2024-05-28 04:48:45 is 34362564.54281222 s in the future tar: ./usr/share/zoneinfo/Canada: time stamp 2024-05-28 04:48:45 is 34362564.54278654 s in the future tar: ./usr/share/zoneinfo/Brazil: time stamp 2024-05-28 04:48:45 is 34362564.54275754 s in the future tar: ./usr/share/zoneinfo/Asia: time stamp 2024-05-28 04:48:45 is 34362564.54272886 s in the future tar: ./usr/share/zoneinfo/Arctic: time stamp 2024-05-28 04:48:45 is 34362564.54269988 s in the future tar: ./usr/share/zoneinfo/Antarctica: time stamp 2024-05-28 04:48:45 is 34362564.54267154 s in the future tar: 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time stamp 2024-05-28 04:48:34 is 34362553.54193702 s in the future tar: ./usr/share/locale/be/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54189332 s in the future tar: ./usr/share/locale/sr/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54184988 s in the future tar: ./usr/share/locale/sr: time stamp 2024-05-28 04:48:14 is 34362533.54182162 s in the future tar: ./usr/share/locale/id/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54179206 s in the future tar: ./usr/share/locale/id: time stamp 2024-05-28 04:48:14 is 34362533.54176334 s in the future tar: ./usr/share/locale/hr/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54173394 s in the future tar: ./usr/share/locale/hr: time stamp 2024-05-28 04:48:14 is 34362533.5417055 s in the future tar: ./usr/share/locale/ga/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54167642 s in the future tar: ./usr/share/locale/ga: time stamp 2024-05-28 04:48:14 is 34362533.54163012 s in the future tar: ./usr/share/locale/et/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54159788 s in the future tar: ./usr/share/locale/et: time stamp 2024-05-28 04:48:14 is 34362533.541569 s in the future tar: ./usr/share/locale/eo/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54153966 s in the future tar: ./usr/share/locale/eo: time stamp 2024-05-28 04:48:14 is 34362533.54151086 s in the future tar: ./usr/share/locale/af/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54148168 s in the future tar: ./usr/share/locale/af: time stamp 2024-05-28 04:48:14 is 34362533.5414533 s in the future tar: ./usr/share/locale/zh_TW/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5414234 s in the future tar: ./usr/share/locale/zh_TW: time stamp 2024-05-28 04:48:14 is 34362533.54139452 s in the future tar: ./usr/share/locale/zh_CN/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54136474 s in the future tar: ./usr/share/locale/zh_CN: time stamp 2024-05-28 04:48:14 is 34362533.5413355 s in the future tar: ./usr/share/locale/vi/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54130582 s in the future tar: ./usr/share/locale/vi: time stamp 2024-05-28 04:48:14 is 34362533.54127734 s in the future tar: ./usr/share/locale/uk/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54124822 s in the future tar: ./usr/share/locale/uk: time stamp 2024-05-28 04:48:14 is 34362533.54122012 s in the future tar: ./usr/share/locale/tr/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54119056 s in the future tar: ./usr/share/locale/tr: time stamp 2024-05-28 04:48:14 is 34362533.5411624 s in the future tar: ./usr/share/locale/sv/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54113564 s in the future tar: ./usr/share/locale/sv: time stamp 2024-05-28 04:48:14 is 34362533.54110754 s in the future tar: ./usr/share/locale/sl/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5410786 s in the future tar: ./usr/share/locale/sl: time stamp 2024-05-28 04:48:14 is 34362533.5410504 s in the future tar: ./usr/share/locale/sk/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54102164 s in the future tar: ./usr/share/locale/sk: time stamp 2024-05-28 04:48:14 is 34362533.54099364 s in the future tar: ./usr/share/locale/ru/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54096402 s in the future tar: ./usr/share/locale/ru: time stamp 2024-05-28 04:48:14 is 34362533.540936 s in the future tar: ./usr/share/locale/ro/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5409068 s in the future tar: ./usr/share/locale/ro: time stamp 2024-05-28 04:48:14 is 34362533.54087896 s in the future tar: ./usr/share/locale/pt_BR/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54084968 s in the future tar: ./usr/share/locale/pt_BR: time stamp 2024-05-28 04:48:14 is 34362533.5408209 s in the future tar: ./usr/share/locale/pt/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5407914 s in the future tar: ./usr/share/locale/pt: time stamp 2024-05-28 04:48:14 is 34362533.54076278 s in the future tar: ./usr/share/locale/pl/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54073368 s in the future tar: ./usr/share/locale/pl: time stamp 2024-05-28 04:48:14 is 34362533.5407055 s in the future tar: ./usr/share/locale/nl/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54067656 s in the future tar: ./usr/share/locale/nl: time stamp 2024-05-28 04:48:14 is 34362533.54064848 s in the future tar: ./usr/share/locale/nb/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5406189 s in the future tar: ./usr/share/locale/nb: time stamp 2024-05-28 04:48:14 is 34362533.54059074 s in the future tar: ./usr/share/locale/lt/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54056202 s in the future tar: ./usr/share/locale/lt: time stamp 2024-05-28 04:48:14 is 34362533.54053382 s in the future tar: ./usr/share/locale/ko/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5405043 s in the future tar: ./usr/share/locale/ko: time stamp 2024-05-28 04:48:14 is 34362533.54047636 s in the future tar: ./usr/share/locale/ja/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54044748 s in the future tar: ./usr/share/locale/ja: time stamp 2024-05-28 04:48:14 is 34362533.54041956 s in the future tar: ./usr/share/locale/it/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54039068 s in the future tar: ./usr/share/locale/it: time stamp 2024-05-28 04:48:14 is 34362533.54036244 s in the future tar: ./usr/share/locale/hu/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54033272 s in the future tar: ./usr/share/locale/hu: time stamp 2024-05-28 04:48:14 is 34362533.54030468 s in the future tar: ./usr/share/locale/gl/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.5402755 s in the future tar: ./usr/share/locale/gl: time stamp 2024-05-28 04:48:14 is 34362533.54024756 s in the future tar: ./usr/share/locale/fr/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54021858 s in the future tar: ./usr/share/locale/fr: time stamp 2024-05-28 04:48:14 is 34362533.54019052 s in the future tar: ./usr/share/locale/fi/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54016122 s in the future tar: ./usr/share/locale/fi: time stamp 2024-05-28 04:48:14 is 34362533.5401327 s in the future tar: ./usr/share/locale/eu/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54010358 s in the future tar: ./usr/share/locale/eu: time stamp 2024-05-28 04:48:14 is 34362533.54007506 s in the future tar: ./usr/share/locale/es/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.54004578 s in the future tar: ./usr/share/locale/es: time stamp 2024-05-28 04:48:14 is 34362533.54001752 s in the future tar: ./usr/share/locale/el/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53998834 s in the future tar: ./usr/share/locale/el: time stamp 2024-05-28 04:48:14 is 34362533.53995974 s in the future tar: ./usr/share/locale/de/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53993044 s in the future tar: ./usr/share/locale/de: time stamp 2024-05-28 04:48:14 is 34362533.53990192 s in the future tar: ./usr/share/locale/da/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53987286 s in the future tar: ./usr/share/locale/da: time stamp 2024-05-28 04:48:14 is 34362533.53984466 s in the future tar: ./usr/share/locale/cs/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53981578 s in the future tar: ./usr/share/locale/cs: time stamp 2024-05-28 04:48:14 is 34362533.53978748 s in the future tar: ./usr/share/locale/ca/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53975804 s in the future tar: ./usr/share/locale/ca: time stamp 2024-05-28 04:48:14 is 34362533.5397301 s in the future tar: ./usr/share/locale/bg/LC_TIME: time stamp 2024-05-28 04:48:34 is 34362553.53970106 s in the future tar: ./usr/share/locale/bg: time stamp 2024-05-28 04:48:14 is 34362533.53967192 s in the future tar: ./usr/lib/apt/planners: time stamp 2024-05-28 04:48:31 is 34362550.52945666 s in the future tar: ./usr/lib/apt: time stamp 2024-05-28 04:48:31 is 34362550.52940794 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/cross-config-5.36.0: time stamp 2024-05-28 04:48:42 is 34362561.52937742 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl: time stamp 2024-05-28 04:48:21 is 34362540.52934706 s in the future tar: ./usr: time stamp 2024-05-28 04:48:26 is 34362545.52929576 s in the future tar: ./run: time stamp 2024-05-28 16:30:22 is 34404661.52927088 s in the future tar: ./etc/systemd/system/multi-user.target.wants: time stamp 2024-05-28 04:48:51 is 34362570.52924246 s in the future tar: ./etc/systemd/system/timers.target.wants: time stamp 2024-05-28 04:48:53 is 34362572.52921208 s in the future tar: ./etc/systemd/system: time stamp 2024-05-28 04:48:51 is 34362570.52918378 s in the future tar: ./etc/rcS.d: time stamp 2024-05-28 04:48:49 is 34362568.52914562 s in the future tar: ./etc/rc6.d: time stamp 2024-05-28 04:48:49 is 34362568.5291198 s in the future tar: ./etc/rc0.d: time stamp 2024-05-28 04:48:49 is 34362568.52909408 s in the future tar: ./etc: time stamp 2024-05-28 16:30:22 is 34404661.52905674 s in the future tar: ./dev: time stamp 2024-05-28 16:30:22 is 34404661.5290327 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 [jellyfish_2.3.0-15.dsc] I: copying [./jellyfish_2.3.0.orig.tar.gz] I: copying [./jellyfish_2.3.0-15.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Sep 28 08:08:02 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.0-15.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in jellyfish-2.3.0 dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.0-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying fix_replacement_of_-L_option.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 dpkg-source: info: applying fix-32-bit.patch dpkg-source: info: applying fix-autoreconf.patch dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11234/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='11234' 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.z9T4hInG/pbuilderrc_MClt --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/b1 --logfile b1/build.log jellyfish_2.3.0-15.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 28 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/11234/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: arm64 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), d-shlibs, autoconf-archive, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on yaggo; however: Package yaggo is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on procps; however: Package procps is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bc{a} bsdextrautils{a} ca-certificates{a} chrpath{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} rake{a} readline-common{a} ruby{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} swig{a} swig4.0{a} time{a} yaggo{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget zip 0 packages upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 49.3 MB of archives. After unpacking 206 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 autoconf-archive all 20220903-3 [775 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 12 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 bc arm64 1.07.1-3 [107 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 d-shlibs all 0.104 [18.6 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 dos2unix arm64 7.4.3-1 [428 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-9 [357 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-9 [466 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B] Get: 83 http://deb.debian.org/debian bookworm/main arm64 rubygems-integration all 1.18 [6704 B] Get: 84 http://deb.debian.org/debian bookworm/main arm64 ruby3.1 arm64 3.1.2-7 [663 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 ruby arm64 1:3.1 [5868 B] Get: 87 http://deb.debian.org/debian bookworm/main arm64 rake all 13.0.6-3 [83.9 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 ruby-sdbm arm64 1.0.0-5+b1 [14.5 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libruby3.1 arm64 3.1.2-7 [5248 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libruby arm64 1:3.1 [4968 B] Get: 95 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B] Get: 99 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B] Get: 102 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 swig4.0 arm64 4.1.0-0.2 [1299 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 swig all 4.1.0-0.2 [321 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 time arm64 1.9-0.2 [50.6 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 yaggo all 1.5.10-6 [21.2 kB] Fetched 49.3 MB in 3s (14.1 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 ... 19616 files and directories currently installed.) Preparing to unpack .../autoconf-archive_20220903-3_all.deb ... Unpacking autoconf-archive (20220903-3) ... Selecting previously unselected package libpython3.11-minimal:arm64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 21114 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 21548 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../04-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../05-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../10-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../11-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../12-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../13-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../14-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../15-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../16-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../17-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../18-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../19-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package bc. Preparing to unpack .../20-bc_1.07.1-3_arm64.deb ... Unpacking bc (1.07.1-3) ... Selecting previously unselected package chrpath. Preparing to unpack .../21-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../22-d-shlibs_0.104_all.deb ... 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Setting up libncurses6:arm64 (6.4-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:arm64 (5.4.1-0.2) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up dos2unix (7.4.3-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up swig4.0 (4.1.0-0.2) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libdeflate-dev:arm64 (1.14-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up chrpath (0.16-2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up swig (4.1.0-0.2) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up bc (1.07.1-3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libcurl3-gnutls:arm64 (7.88.1-9) ... Setting up rubygems-integration (1.18) ... Setting up libcurl4-gnutls-dev:arm64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libhts-dev:arm64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up samtools (1.16.1-1) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-all (3.11.2-1+b1) ... Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up rake (13.0.6-3) ... Setting up ruby3.1 (3.1.2-7) ... Setting up libruby3.1:arm64 (3.1.2-7) ... Setting up libruby:arm64 (1:3.1) ... Setting up ruby (1:3.1) ... Setting up yaggo (1.5.10-6) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b1) ... Setting up ruby-rubygems (3.3.15-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... 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/jellyfish-2.3.0/ && 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 > ../jellyfish_2.3.0-15_source.changes dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.0-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/jellyfish-2.3.0' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so rm -f swig/perl5/blib/bin/.exists rm -f swig/perl5/blib/lib/.exists rm -f swig/perl5/blib/lib/auto/jellyfish/.exists rm -f swig/perl5/blib/man1/.exists rm -f swig/perl5/blib/man3/.exists rm -f swig/perl5/blib/script/.exists rm -f swig/perl5/jellyfish.bs rm -f swig/perl5/pm_to_blib rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/ make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules binary dh binary --with python3 debian/rules override_dh_update_autotools_config make[1]: Entering directory '/build/jellyfish-2.3.0' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/build/jellyfish-2.3.0' 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:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:65: warning: The macro `AC_TRY_RUN' is obsolete. configure.ac:65: You should run autoupdate. ./lib/autoconf/general.m4:2997: AC_TRY_RUN is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... m4/m4-ax_ext.m4:49: AX_EXT is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... configure.ac:65: the top level configure.ac:107: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:107: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:107: the top level configure.ac:118: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:118: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:118: the top level configure.ac:121: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:121: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:121: the top level configure.ac:124: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:124: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:124: the top level configure.ac:127: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:127: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:127: the top level configure.ac:131: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:131: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:131: the top level configure.ac:135: warning: The macro `SWIG_ENABLE_CXX' is obsolete. configure.ac:135: You should run autoupdate. m4/m4-ax_swig_enable_cxx.m4:48: SWIG_ENABLE_CXX is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... configure.ac:135: the top level configure.ac:145: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:145: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:145: the top level configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/jellyfish-2.3.0' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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 whether make supports nested variables... (cached) yes 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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-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... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes 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 checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.1.0 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.11 checking for Python library path... -L/usr/lib/aarch64-linux-gnu -lpython3.11 checking for Python site-packages path... /usr/lib/python3.11/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.11/site-packages checking python extra libraries... -ldl -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/aarch64-linux-gnu/perl/5.36/CORE checking for Perl extension target directory... /usr/lib/perl/5.36.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" -I/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config /build/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/jellyfish-2.3.0' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/build/jellyfish-2.3.0' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. 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-Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o `test -f 'unit_tests/test_mer_dna_bloom_counter.cc' || echo './'`unit_tests/test_mer_dna_bloom_counter.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_whole_sequence_parser.o `test -f 'unit_tests/test_whole_sequence_parser.cc' || echo './'`unit_tests/test_whole_sequence_parser.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_allocators_mmap.o `test -f 'unit_tests/test_allocators_mmap.cc' || echo './'`unit_tests/test_allocators_mmap.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_cooperative_pool2.o `test -f 'unit_tests/test_cooperative_pool2.cc' || echo './'`unit_tests/test_cooperative_pool2.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_generator_manager.o `test -f 'unit_tests/test_generator_manager.cc' || echo './'`unit_tests/test_generator_manager.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_atomic_bits_array.o `test -f 'unit_tests/test_atomic_bits_array.cc' || echo './'`unit_tests/test_atomic_bits_array.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/bin_test_all-test_stdio_filebuf.o `test -f 'unit_tests/test_stdio_filebuf.cc' || echo './'`unit_tests/test_stdio_filebuf.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -DJSON_IS_AMALGAMATION=1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/bin_test_all-backtrace.o `test -f 'jellyfish/backtrace.cc' || echo './'`jellyfish/backtrace.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_la-gtest-all.lo `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o unit_tests/gtest/src/gtest-all.cc: In function 'bool testing::internal::StackGrowsDown()': unit_tests/gtest/src/gtest-all.cc:7485:24: warning: 'dummy' may be used uninitialized [-Wmaybe-uninitialized] 7485 | StackLowerThanAddress(&dummy, &result); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ unit_tests/gtest/src/gtest-all.cc:7477:6: note: by argument 1 of type 'const void*' to 'void testing::internal::StackLowerThanAddress(const void*, bool*)' declared here 7477 | void StackLowerThanAddress(const void* ptr, bool* result) { | ^~~~~~~~~~~~~~~~~~~~~ unit_tests/gtest/src/gtest-all.cc:7483:7: note: 'dummy' declared here 7483 | int dummy; | ^~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest-all.cc -o unit_tests/gtest/src/libgtest_la-gtest-all.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -I./unit_tests/gtest -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest.la unit_tests/gtest/src/libgtest_la-gtest-all.lo libtool: link: ar cr .libs/libgtest.a unit_tests/gtest/src/.libs/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest.a libtool: link: ( cd ".libs" && rm -f "libgtest.la" && ln -s "../libgtest.la" "libgtest.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j8 make[2]: Entering directory '/build/jellyfish-2.3.0/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/aarch64-linux-gnu/perl/5.36/CORE" swig_wrap.cpp chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ -lpthread \ chmod 755 blib/arch/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-2.3.0/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build build_ext -L/build/jellyfish-2.3.0/.libs /build/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running build running build_py copying dna_jellyfish.py -> /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-arm64-3.11 aarch64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0 -I/usr/include/python3.11 -c swig_wrap.cpp -o build/temp.linux-arm64-3.11/swig_wrap.o -std=c++0x aarch64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.11/swig_wrap.o -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/build/jellyfish-2.3.0/.libs -ljellyfish-2.0 -lpthread -o /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-aarch64-linux-gnu.so -Wl,-rpath,/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu make[1]: Leaving directory '/build/jellyfish-2.3.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/jellyfish-2.3.0' dh_auto_test make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 make[2]: Entering directory '/build/jellyfish-2.3.0' make check-am make[3]: Entering directory '/build/jellyfish-2.3.0' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/build/jellyfish-2.3.0' make[4]: 'bin/generate_sequence' is up to date. make[4]: 'bin/fastq2sam' is up to date. make[4]: 'bin/test_all' is up to date. make[4]: 'libgtest.la' is up to date. /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -pthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -lhts -R/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/build/jellyfish-2.3.0/./.libs/libgtest.a") libtool: link: ar cr .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest_main.a libtool: link: rm -fr .libs/libgtest_main.lax libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" ) make[4]: Leaving directory '/build/jellyfish-2.3.0' make check-TESTS make[4]: Entering directory '/build/jellyfish-2.3.0' make[5]: Entering directory '/build/jellyfish-2.3.0' SKIP: tests/big.sh PASS: tests/generate_sequence.sh PASS: tests/subset_hashing.sh PASS: tests/bloom_filter.sh PASS: tests/bloom_counter.sh PASS: tests/swig_python.sh SKIP: tests/swig_ruby.sh PASS: tests/large_key.sh PASS: tests/multi_file.sh PASS: tests/sam.sh PASS: tests/small_mers.sh PASS: tests/merge.sh PASS: tests/swig_perl.sh PASS: tests/parallel_hashing.sh PASS: unit_tests/unit_tests.sh ============================================================================ Testsuite summary for jellyfish 2.3.0 ============================================================================ # TOTAL: 15 # PASS: 13 # SKIP: 2 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/jellyfish-2.3.0' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' make[2]: Leaving directory '/build/jellyfish-2.3.0' make[1]: Leaving directory '/build/jellyfish-2.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/jellyfish-2.3.0' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/build/jellyfish-2.3.0' make install-am make[3]: Entering directory '/build/jellyfish-2.3.0' make[4]: Entering directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish-2.3.0/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish-2.3.0/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[4]: Leaving directory '/build/jellyfish-2.3.0' make[3]: Leaving directory '/build/jellyfish-2.3.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/build/jellyfish-2.3.0/debian/tmp/usr/include/jellyfish-2.3.0/jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish-2.3.0/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.36.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/build/jellyfish-2.3.0/debian/tmp/usr/lib/perl/5.36.0' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /build/jellyfish-2.3.0; /bin/bash "/build/jellyfish-2.3.0/libtool" --tag CXX --mode=relink g++ -I/build/jellyfish-2.3.0/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -ffile-prefix-map=/build/jellyfish-2.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-nonnull -module -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.11/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /build/jellyfish-2.3.0/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/build/jellyfish-2.3.0/debian/tmp/usr/lib/python3.11/site-packages/dna_jellyfish' make[2]: Leaving directory '/build/jellyfish-2.3.0' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/jellyfish-2.3.0/debian/python3-dna-jellyfish /build/jellyfish-2.3.0/swig/python/setup.py:12: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup, Extension running install running build running build_py running build_ext running install_lib creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11 creating /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/_dna_jellyfish.cpython-311-aarch64-linux-gnu.so -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages copying /build/jellyfish-2.3.0/.pybuild/cpython3_3.11_dna_jellyfish/build/dna_jellyfish.py -> /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages byte-compiling /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-311.pyc running install_egg_info Writing /build/jellyfish-2.3.0/debian/python3-dna-jellyfish/usr/lib/python3.11/dist-packages/dna_jellyfish-0.0.1.egg-info dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j8 install DESTDIR=/build/jellyfish-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/jellyfish-2.3.0/swig/perl5' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.36/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/build/jellyfish-2.3.0/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 pbuilder1 pbuilder1 1197384 Apr 26 11:50 debian/tmp/usr/lib/aarch64-linux-gnu/perl5/5.36/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu || true mv debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu mv /build/jellyfish-2.3.0/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/aarch64-linux-gnu PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/aarch64-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/build/jellyfish-2.3.0' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/jellyfish-2.3.0' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.* dh_missing make[1]: Leaving directory '/build/jellyfish-2.3.0' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.0-15_arm64.deb'. dpkg-deb: building package 'libjellyfish-perl-dbgsym' in '../libjellyfish-perl-dbgsym_2.3.0-15_arm64.deb'. dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.0-15_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish-dbgsym' in '../python3-dna-jellyfish-dbgsym_2.3.0-15_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.0-15_arm64.deb'. dpkg-deb: building package 'libjellyfish-2.0-2-dbgsym' in '../libjellyfish-2.0-2-dbgsym_2.3.0-15_arm64.deb'. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.0-15_all.deb'. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.0-15_arm64.deb'. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.0-15_arm64.deb'. dpkg-deb: building package 'jellyfish-dbgsym' in '../jellyfish-dbgsym_2.3.0-15_arm64.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.0-15_arm64.buildinfo dpkg-genchanges --build=binary -O../jellyfish_2.3.0-15_arm64.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: not including original 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/11234 and its subdirectories I: Current time: Wed Apr 26 11:55:02 -12 2023 I: pbuilder-time-stamp: 1682553302 Wed Apr 26 23:55:05 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Wed Apr 26 23:55:05 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Thu Apr 27 00:22:31 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Thu Apr 27 00:22:32 UTC 2023 I: jellyfish_2.3.0-15_arm64.changes: Format: 1.8 Date: Wed, 28 Sep 2022 21:48:56 +0200 Source: jellyfish Binary: jellyfish jellyfish-dbgsym jellyfish-examples libjellyfish-2.0-2 libjellyfish-2.0-2-dbgsym libjellyfish-2.0-dev libjellyfish-perl libjellyfish-perl-dbgsym python3-dna-jellyfish python3-dna-jellyfish-dbgsym Architecture: arm64 all Version: 2.3.0-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish) libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish) libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish) python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish) Closes: 1017261 Changes: jellyfish (2.3.0-15) unstable; urgency=medium . * Fix dh_missing Closes: #1017261 Checksums-Sha1: e7f4644e0762f9c83cb9aa21fd8955b82ea2db0c 7907564 jellyfish-dbgsym_2.3.0-15_arm64.deb a635444e1265f8c170da736d6406eb5e98d81105 12964 jellyfish-examples_2.3.0-15_all.deb 6e223e4bbef1327f1f25d86dbc9e30665b36eb40 10253 jellyfish_2.3.0-15_arm64.buildinfo aadcc5c72ec3279af27aef71e30c9f2e433960fb 704036 jellyfish_2.3.0-15_arm64.deb d3c51b3aa32cd8b01b78acfbc3620cae8f3212cb 529632 libjellyfish-2.0-2-dbgsym_2.3.0-15_arm64.deb 416e8d0f0144e18066896a17da2571db2632d43a 58340 libjellyfish-2.0-2_2.3.0-15_arm64.deb f359d9f5ba1d59953dc63b28a89c9e909443e5a7 132820 libjellyfish-2.0-dev_2.3.0-15_arm64.deb d022fdd23b6a51ccff44407f2aa6754e63892743 349928 libjellyfish-perl-dbgsym_2.3.0-15_arm64.deb eb8cfc213a724884388c035400f71e5d9467c5e6 49488 libjellyfish-perl_2.3.0-15_arm64.deb 70b2e091a62cb2ff7cb66341bc7d1c2474e7ff42 333920 python3-dna-jellyfish-dbgsym_2.3.0-15_arm64.deb 54d5d25302fbcf6ed754551784da2294f21597de 50756 python3-dna-jellyfish_2.3.0-15_arm64.deb Checksums-Sha256: db958d15dc1d48b2ba0d9e0da41cfdd145924ec4c7c5c7fb12bcd47a3e7d7003 7907564 jellyfish-dbgsym_2.3.0-15_arm64.deb 3c0cccc3f6e059a379fb08934e815e5352993636c3f527fc30251b2504eb97d0 12964 jellyfish-examples_2.3.0-15_all.deb a746c54ef00587a90eaa50383a8901255722c3e0930c5980ca01e4d02949576a 10253 jellyfish_2.3.0-15_arm64.buildinfo 3923054fd11af0511577f62004445ece5b06aa8499cdaf82cb4405f801e2448e 704036 jellyfish_2.3.0-15_arm64.deb ccc3885e37f69dae07367b9f2f5a688cb9317b7927864e506d33f9a40c85e0b9 529632 libjellyfish-2.0-2-dbgsym_2.3.0-15_arm64.deb 8c12d0a2a980c7add5bf407a0d1056e33f3cc380660ce12abf66bbb87c64e86d 58340 libjellyfish-2.0-2_2.3.0-15_arm64.deb 1e6f0413d6a23ead3c784a504a4cb28f8549f7b559f3e6b928f549a5e2472c9f 132820 libjellyfish-2.0-dev_2.3.0-15_arm64.deb 13695fbe2e5908a41fff8eb84b605b5c344199551777b99abcaaef9b57ee647d 349928 libjellyfish-perl-dbgsym_2.3.0-15_arm64.deb 61763e54dd22f8811eb730b870b35af44ef42a6422d5aae71e78879ad04632e7 49488 libjellyfish-perl_2.3.0-15_arm64.deb e88e41e9e0d1d33a5f0591842e58f46ca019841717af07f19d9b8144047b9580 333920 python3-dna-jellyfish-dbgsym_2.3.0-15_arm64.deb a726c8855efe9cfb6ac79cdd195e80c85be13f58252c12b264617626493e3ff1 50756 python3-dna-jellyfish_2.3.0-15_arm64.deb Files: 851e649986606e5c258278d71befee95 7907564 debug optional jellyfish-dbgsym_2.3.0-15_arm64.deb 02d5ceb4636a832fc4a8e27cbc6c2706 12964 science optional jellyfish-examples_2.3.0-15_all.deb d5268113b0fc6a13b20a8a28de06d605 10253 science optional jellyfish_2.3.0-15_arm64.buildinfo 85cb985465944da953b3adc889aa9a5f 704036 science optional jellyfish_2.3.0-15_arm64.deb a14fdd4d436838ab183fed83d0648c68 529632 debug optional libjellyfish-2.0-2-dbgsym_2.3.0-15_arm64.deb ab1b816c4b9b9349fa9d2bf3816531d3 58340 libs optional libjellyfish-2.0-2_2.3.0-15_arm64.deb 5144b1535d15e21e05483257f008b37a 132820 libdevel optional libjellyfish-2.0-dev_2.3.0-15_arm64.deb 4f6ee61e68da8a73e0af474ea778d5c2 349928 debug optional libjellyfish-perl-dbgsym_2.3.0-15_arm64.deb 2a8b633c07c3c4fb5e0b4c4434636090 49488 perl optional libjellyfish-perl_2.3.0-15_arm64.deb 5f0077325321caca8a2b89a1637c3d43 333920 debug optional python3-dna-jellyfish-dbgsym_2.3.0-15_arm64.deb b3b03811ea7af2409c641248b0fad4b7 50756 python optional python3-dna-jellyfish_2.3.0-15_arm64.deb Thu Apr 27 00:22:34 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/jellyfish_2.3.0-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/jellyfish_2.3.0-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/jellyfish_2.3.0-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/b1/jellyfish_2.3.0-15_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.z9T4hInG/b2/jellyfish_2.3.0-15_arm64.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: 0.467s) 0.467s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.136s) 0.136s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Thu Apr 27 00:22:35 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 27 00:22:35 UTC 2023 I: jellyfish from bookworm built successfully and reproducibly on arm64. Thu Apr 27 00:22:36 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Apr 27 00:22:36 UTC 2023 I: Submitting 12K b1/jellyfish_2.3.0-15_arm64.buildinfo.asc Thu Apr 27 00:22:38 UTC 2023 I: Submitting 12K b2/jellyfish_2.3.0-15_arm64.buildinfo.asc Thu Apr 27 00:22:39 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 27 00:22:39 UTC 2023 I: Done submitting .buildinfo files. Thu Apr 27 00:22:39 UTC 2023 I: Removing signed jellyfish_2.3.0-15_arm64.buildinfo.asc files: removed './b1/jellyfish_2.3.0-15_arm64.buildinfo.asc' removed './b2/jellyfish_2.3.0-15_arm64.buildinfo.asc'