sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Tue, 01 Jul 2025 18:16:41 +0000 | +==============================================================================+ Package: proteinortho Version: 6.3.1+dfsg-1 Source Version: 6.3.1+dfsg-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 01 Jul 2025 18:16:41 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup proteinortho_6.3.1+dfsg-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup proteinortho_6.3.1+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 01 Jul 2025 18:16:42 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://deb.debian.org/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Tue, 01 Jul 2025 18:16:48 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 01 Jul 2025 18:16:48 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper, build-essential Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner (>= 2.0.10~), procps, debhelper, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive ./ InRelease Get:2 copy:/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive ./ Release [609 B] Ign:3 copy:/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive ./ Release.gpg Get:4 copy:/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive ./ Sources [712 B] Get:5 copy:/build/proteinortho-1w4Ong/resolver-hWzQsh/apt_archive ./ Packages [716 B] Fetched 2037 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgfortran5 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support Recommended packages: med-config curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism diamond-aligner dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgfortran5 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data ncbi-vdb-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 51.0 MB of archives. After this operation, 221 MB of additional disk space will be used. 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amd64 libpython3-stdlib amd64 3.13.5-1 [10.2 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.5-1 [28.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-8 [65.4 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-8 [881 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-7 [16.0 MB] Preconfiguring packages ... 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Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up diamond-aligner (2.1.11-2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jul 1 18:16:58 UTC 2025. Universal Time is now: Tue Jul 1 18:16:58 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libproc2-0:amd64 (2:4.0.4-8) ... Setting up autopoint (0.23.1-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up ncbi-vdb-data (3.2.1+dfsg-2) ... Setting up netbase (6.5) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libmbedcrypto16:amd64 (3.6.3-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libpython3-stdlib:amd64 (3.13.5-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up python3.13 (3.13.5-2) ... Setting up python3 (3.13.5-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.3-1) ... Setting up liblapack-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libmbedtls21:amd64 (3.6.3-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-7) ... Setting up debhelper (13.24.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 01 Jul 2025 18:17:00 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Tue, 01 Jul 2025 18:17:00 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 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gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.44-3 libblas-dev_3.12.1-2 libblas3_3.12.1-2 libblkid1_2.41-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 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+------------------------------------------------------------------------------+ | Build Tue, 01 Jul 2025 18:17:00 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 6.3.1+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev | libatlas-base-dev | liblapack.so, diamond-aligner (>= 2.0.10~), procps, debhelper Package-List: proteinortho deb science optional arch=any Checksums-Sha1: 36ddff1bcbf8dde0a19795f74e154e74aadc1705 375988 proteinortho_6.3.1+dfsg.orig.tar.xz d2526cacd7835c2f294f0219e9514a1644f13e78 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Checksums-Sha256: 7ce978cf6d33a6f67a3138d7f4cafe3ed5c1dcfbdd70224f1514385df9531679 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ab190de700fdc10752e33b2e0c263f6166a2dfb8d8a119d987a7265b99df61fe 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz Files: 286e6fd86b91807e92db7e8bd7a3c87c 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ee4d531727d1dc02b1af12b004ed1c99 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWg1C8RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHolg/8CJZu3mudXnpM0z+TV/H6OgBg+eGm/mkU opYsSgqwFb4k6PwHTa9VA3Zq+liUKDRLBvRyz0olnOff5RhE5t+xys2LMHLj+n4g Maij/jnhq+XbAefm4Z0MFg4LsVH/rrKCn+fWlCV7H4YoKL/QEkbsIebdD4l+7jhV qe1cMgEHjmG+6XccBmpii+dLyIQGGuRGIIdmaOzmxPw8EzFQkE7uOdhWG42PtPgo YVM/JZyLXe7gtY73UM8MFOTIuJ/RVOwx/BUOjuC6P9zu0TimNhwBnNvwQW+PECu5 nJWgm1mixkpGvsQSNsu7ITUPMbbr/LE9Vu7yt/1V28SbCQxgsNwuONG1+Qyao3lt 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Commands Tue, 01 Jul 2025 18:17:01 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network proteinortho_6.3.1+dfsg-1 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network proteinortho_6.3.1+dfsg-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-caf14100-9cd6-4aad-8066-d1764e1d409e SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 6.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' rm -rf src/BUILD test/C*.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.* rm -rf src/lapack-3.8.0/ make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building proteinortho using existing ./proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building proteinortho in proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: building proteinortho in proteinortho_6.3.1+dfsg-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j2 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = CXX = Creating build directory ... g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection MTUNEARCHFLAGS = LDFLAGS = -Wl,-z,relro -Wl,-z,now LDLIBS = STATIC = FALSE [ 10%] Prepare proteinortho_clustering ... [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fopenmp -o src/BUILD/Linux_x86_64/proteinortho_clustering src/proteinortho_clustering.cpp -Wl,-z,relro -Wl,-z,now -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive [ 25%] Building **graphMinusRemovegraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph src/graphMinusRemovegraph.cpp -Wl,-z,relro -Wl,-z,now [ 50%] Building **cleanupblastgraph** g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph src/cleanupblastgraph.cpp -Wl,-z,relro -Wl,-z,now - test max_of_diag() : OK - test generate_random_vector() : OK - test get_new_x() : OK - test makeOrthogonal() : OK - test normalize() : OK - test getY() : OK - test lapack() : OK - test power() : OK - test smirnov-grubb() : OK All test passed. ......OK dynamic linking was successful for proteinortho_clustering! [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' [TEST] Clean up all test files... [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) [1/12] -p=blastp test: passed [2/12] -p=blastp+ synteny (PoFF) test: tput: No value for $TERM and no -T specified tput: No value for $TERM and no -T specified tput: No value for $TERM and no -T specified tput: No value for $TERM and no -T specified passed [3/12] -p=diamond test: passed [4/12] -p=diamond (--moresensitive) test (subparaBlast): passed [5/12] -p=lastp (lastal) test: lastal missing, skipping... [6/12] -p=topaz test: topaz missing, skipping... [7/12] -p=usearch test: usearch missing, skipping... [8/12] -p=ublast test: usearch missing, skipping... [9/12] -p=rapsearch test: rapsearch missing, skipping... [10/12] -p=blatp (blat) test: blat missing, skipping... [11/12] -p=mmseqsp (mmseqs) test: mmseqs missing, skipping... [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: passed [TEST] Clean up all test files... ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; [TEST] 2. -step=3 tests (proteinortho_clustering) [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): passed [2/6] Test proteinortho_clustering using lapack: passed [3/6] Test proteinortho_clustering using power: passed [4/6] Test proteinortho_clustering using lapack and no weights: passed [5/6] Test proteinortho_clustering using maxnodes/flooding: passed [6/6] Test proteinortho_clustering using no clustering at all: passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 0 test/ring4_K5.blast-graph >test_power_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_power_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/ring4_K5.blast-graph >test_lapack_ring4_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_ring4_K5.proteinortho.tsv "ring4_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P3_K5.blast-graph >test_lapack_P3_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P3_K5.proteinortho.tsv "P3_K5"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/P4.blast-graph >test_lapack_P4.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_P4.proteinortho.tsv "P4"; passed OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 test/K5.blast-graph >test_lapack_K5.proteinortho.tsv 2>/dev/null ; \ set -e ; ./src/chk_test.pl test_lapack_K5.proteinortho.tsv "K5"; passed ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa 2>/dev/null; testing if there is a protein that occurs twice in the output: passed ./proteinortho6.pl -silent -force -singles -project=test_singles_diamond -p=diamond test/*.faa 2>/dev/null; testing if all proteins are in the output (using -singles): set -e ; diff test_singles_diamond.true test_singles_diamond.test; passed [TEST] All tests passed make[2]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' mkdir -p /build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin make -j2 install DESTDIR=/build/proteinortho-1w4Ong/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/proteinortho-1w4Ong/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho' in '../proteinortho_6.3.1+dfsg-1_amd64.deb'. dpkg-genbuildinfo -O../proteinortho_6.3.1+dfsg-1_amd64.buildinfo dpkg-genchanges -O../proteinortho_6.3.1+dfsg-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-07-01T18:18:33Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 01 Jul 2025 18:18:33 +0000 | +------------------------------------------------------------------------------+ proteinortho_6.3.1+dfsg-1_amd64.changes: ---------------------------------------- Format: 1.8 Date: Fri, 12 Jan 2024 06:50:22 +0100 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: source amd64 Version: 6.3.1+dfsg-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: proteinortho - Detection of (Co-)orthologs in large-scale protein analysis Closes: 1046514 Changes: proteinortho (6.3.1+dfsg-1) unstable; urgency=medium . * New upstream version * Clean up after testing Closes: #1046514 Checksums-Sha1: b9f9d30d0130b3c262a0d767e4d5320bd67ddba1 1253 proteinortho_6.3.1+dfsg-1.dsc 36ddff1bcbf8dde0a19795f74e154e74aadc1705 375988 proteinortho_6.3.1+dfsg.orig.tar.xz d2526cacd7835c2f294f0219e9514a1644f13e78 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz a47e695b0ee06967ff6f317a5e094df7763bffa7 1983120 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 257f512e4ff4dc8285c2873a536e4ffdf0dede31 6313 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 5d723daba7b77147505bd85ef3d84c12fec43082 364236 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 264c5e85f99730d28128c7fdff728f16b79a73f3cd83374c108c17501250ee3b 1253 proteinortho_6.3.1+dfsg-1.dsc 7ce978cf6d33a6f67a3138d7f4cafe3ed5c1dcfbdd70224f1514385df9531679 375988 proteinortho_6.3.1+dfsg.orig.tar.xz ab190de700fdc10752e33b2e0c263f6166a2dfb8d8a119d987a7265b99df61fe 7248 proteinortho_6.3.1+dfsg-1.debian.tar.xz ed074ff1e4385d6cdfe97ff6cf59625e5447616667c3b00e6a3b97cd0ee79ce8 1983120 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb eb49f8809ac79ab03a7bbaf72c38d3b0f9524f77626b4980790f1bebb7dea6fa 6313 proteinortho_6.3.1+dfsg-1_amd64.buildinfo e43811f8f749ad60ff3985337a1547532bff4365ceb0d594d2c04767aaac856e 364236 proteinortho_6.3.1+dfsg-1_amd64.deb Files: 50b7ea772bf552883ed47b4130ec18f8 1253 science optional proteinortho_6.3.1+dfsg-1.dsc 286e6fd86b91807e92db7e8bd7a3c87c 375988 science optional proteinortho_6.3.1+dfsg.orig.tar.xz ee4d531727d1dc02b1af12b004ed1c99 7248 science optional proteinortho_6.3.1+dfsg-1.debian.tar.xz 180addc3e13f5736af412882f7cee314 1983120 debug optional proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 9369fa56150d590e94e59431c3f2d4db 6313 science optional proteinortho_6.3.1+dfsg-1_amd64.buildinfo ac793e7e072eda88a9f67678425968e1 364236 science optional proteinortho_6.3.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 01 Jul 2025 18:18:34 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: amd64 source Version: 6.3.1+dfsg-1 Checksums-Md5: 50b7ea772bf552883ed47b4130ec18f8 1253 proteinortho_6.3.1+dfsg-1.dsc 180addc3e13f5736af412882f7cee314 1983120 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb ac793e7e072eda88a9f67678425968e1 364236 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha1: b9f9d30d0130b3c262a0d767e4d5320bd67ddba1 1253 proteinortho_6.3.1+dfsg-1.dsc a47e695b0ee06967ff6f317a5e094df7763bffa7 1983120 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 5d723daba7b77147505bd85ef3d84c12fec43082 364236 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 264c5e85f99730d28128c7fdff728f16b79a73f3cd83374c108c17501250ee3b 1253 proteinortho_6.3.1+dfsg-1.dsc ed074ff1e4385d6cdfe97ff6cf59625e5447616667c3b00e6a3b97cd0ee79ce8 1983120 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb e43811f8f749ad60ff3985337a1547532bff4365ceb0d594d2c04767aaac856e 364236 proteinortho_6.3.1+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 01 Jul 2025 18:18:33 +0000 Build-Path: /build/proteinortho-1w4Ong/proteinortho-6.3.1+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diamond-aligner (= 2.1.11-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.44-3), libblas-dev (= 3.12.1-2), libblas3 (= 3.12.1-2), libblkid1 (= 2.41-5), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libexpat1 (= 2.7.1-1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-19), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libhwasan0 (= 14.2.0-19), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), liblapack-dev (= 3.12.1-2), liblapack3 (= 3.12.1-2), liblastlog2-2 (= 2.41-5), liblmdb0 (= 0.9.31-1+b2), liblsan0 (= 14.2.0-19), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmbedcrypto16 (= 3.6.3-1), libmbedtls21 (= 3.6.3-1), libmbedx509-7 (= 3.6.3-1), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libncbi-vdb3 (= 3.2.1+dfsg-2), libncursesw6 (= 6.5+20250216-2), libnghttp2-14 (= 1.64.0-1.1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libproc2-0 (= 2:4.0.4-8), libpython3-stdlib (= 3.13.5-1), libpython3.13-minimal (= 3.13.5-2), libpython3.13-stdlib (= 3.13.5-2), libquadmath0 (= 14.2.0-19), libreadline8t64 (= 8.2-6), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libuv1t64 (= 1.50.0-2), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 13.0.0), ncbi-blast+ (= 2.16.0+ds-7), ncbi-data (= 6.1.20170106+dfsg2-6), ncbi-vdb-data (= 3.2.1+dfsg-2), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-8), python3 (= 3.13.5-1), python3-minimal (= 3.13.5-1), python3.13 (= 3.13.5-2), python3.13-minimal (= 3.13.5-2), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-4), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1705038622" +------------------------------------------------------------------------------+ | Package contents Tue, 01 Jul 2025 18:18:34 +0000 | +------------------------------------------------------------------------------+ proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 1983120 bytes: control archive=696 bytes. 483 bytes, 12 lines control 407 bytes, 4 lines md5sums Package: proteinortho-dbgsym Source: proteinortho Version: 6.3.1+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2108 Depends: proteinortho (= 6.3.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for proteinortho Build-Ids: 12dbc49199f7b4aa7335e2ba1b79ce690e7b9fd8 44382ccd04de7563b0647148cdc2bbfdb7b24087 e588f855572f9549f6a2fc92e33ada18e33f3195 drwxr-xr-x root/root 0 2024-01-12 05:50 ./ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/12/ -rw-r--r-- root/root 126840 2024-01-12 05:50 ./usr/lib/debug/.build-id/12/dbc49199f7b4aa7335e2ba1b79ce690e7b9fd8.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/44/ -rw-r--r-- root/root 149720 2024-01-12 05:50 ./usr/lib/debug/.build-id/44/382ccd04de7563b0647148cdc2bbfdb7b24087.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/e5/ -rw-r--r-- root/root 1842808 2024-01-12 05:50 ./usr/lib/debug/.build-id/e5/88f855572f9549f6a2fc92e33ada18e33f3195.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 22536 2024-01-12 05:50 ./usr/lib/debug/.dwz/x86_64-linux-gnu/proteinortho.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-01-12 05:50 ./usr/share/doc/proteinortho-dbgsym -> proteinortho proteinortho_6.3.1+dfsg-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 364236 bytes: control archive=1836 bytes. 985 bytes, 17 lines control 2467 bytes, 34 lines md5sums Package: proteinortho Version: 6.3.1+dfsg-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1213 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), liblapack3, libstdc++6 (>= 13.1), perl:any, python3, ncbi-blast+, diamond-aligner (>= 2.0.10~), procps Section: science Priority: optional Homepage: https://gitlab.com/paulklemm_PHD/proteinortho Description: Detection of (Co-)orthologs in large-scale protein analysis Proteinortho is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. Proteinortho was applied to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. Authors succeeded identifying thirty proteins present in 99% of all bacterial proteomes. drwxr-xr-x root/root 0 2024-01-12 05:50 ./ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/bin/ lrwxrwxrwx root/root 0 2024-01-12 05:50 ./usr/bin/proteinortho -> proteinortho6.pl -rwxr-xr-x root/root 38800 2024-01-12 05:50 ./usr/bin/proteinortho2html.pl -rwxr-xr-x root/root 4997 2024-01-12 05:50 ./usr/bin/proteinortho2tree.pl -rwxr-xr-x root/root 8439 2024-01-12 05:50 ./usr/bin/proteinortho2xml.pl -rwxr-xr-x root/root 250453 2024-01-12 05:50 ./usr/bin/proteinortho6.pl -rwxr-xr-x root/root 43408 2024-01-12 05:50 ./usr/bin/proteinortho_cleanupblastgraph -rwxr-xr-x root/root 485848 2024-01-12 05:50 ./usr/bin/proteinortho_clustering -rwxr-xr-x root/root 1239 2024-01-12 05:50 ./usr/bin/proteinortho_compareProteinorthoGraphs.pl -rwxr-xr-x root/root 9152 2024-01-12 05:50 ./usr/bin/proteinortho_do_mcl.pl -rwxr-xr-x root/root 1166 2024-01-12 05:50 ./usr/bin/proteinortho_extract_from_graph.pl -rwxr-xr-x root/root 32942 2024-01-12 05:50 ./usr/bin/proteinortho_ffadj_mcs.py -rwxr-xr-x root/root 479 2024-01-12 05:50 ./usr/bin/proteinortho_formatUsearch.pl -rwxr-xr-x root/root 17618 2024-01-12 05:50 ./usr/bin/proteinortho_grab_proteins.pl -rwxr-xr-x root/root 35224 2024-01-12 05:50 ./usr/bin/proteinortho_graphMinusRemovegraph -rwxr-xr-x root/root 30708 2024-01-12 05:50 ./usr/bin/proteinortho_history.pl -rwxr-xr-x root/root 2383 2024-01-12 05:50 ./usr/bin/proteinortho_singletons.pl -rwxr-xr-x root/root 14766 2024-01-12 05:50 ./usr/bin/proteinortho_summary.pl drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/proteinortho/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/doc/proteinortho/ -rw-r--r-- root/root 263 2024-01-12 05:50 ./usr/share/doc/proteinortho/README.test -rw-r--r-- root/root 1955 2024-01-12 05:50 ./usr/share/doc/proteinortho/changelog.Debian.gz -rw-r--r-- root/root 13213 2023-12-11 14:47 ./usr/share/doc/proteinortho/changelog.gz -rw-r--r-- root/root 1095 2024-01-12 05:50 ./usr/share/doc/proteinortho/copyright drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/doc/proteinortho/examples/ -rw-r--r-- root/root 52860 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/C.faa -rw-r--r-- root/root 18472 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/C.gff -rw-r--r-- root/root 752 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/C2.faa -rw-r--r-- root/root 120 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/C2.gff -rw-r--r-- root/root 55942 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/E.faa -rw-r--r-- root/root 18666 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/E.gff -rw-r--r-- root/root 27375 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/L.faa -rw-r--r-- root/root 2376 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/L.gff -rw-r--r-- root/root 27690 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/M.faa -rw-r--r-- root/root 2317 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/M.gff -rwxr-xr-x root/root 1205 2023-12-11 14:47 ./usr/share/doc/proteinortho/examples/chk_test.pl -rw-r--r-- root/root 2371 2024-01-12 05:50 ./usr/share/doc/proteinortho/run-unit-test drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 109 2024-01-12 05:50 ./usr/share/lintian/overrides/proteinortho drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2024-01-12 05:50 ./usr/share/man/man1/proteinortho.1.gz -> proteinortho6.1.gz -rw-r--r-- root/root 1562 2024-01-12 05:50 ./usr/share/man/man1/proteinortho6.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 01 Jul 2025 18:18:34 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 01 Jul 2025 18:18:34 +0000 | +------------------------------------------------------------------------------+ Purging /build/proteinortho-1w4Ong Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 01 Jul 2025 18:18:35 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 16308 Build-Time: 92 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 12 Job: /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: proteinortho Package-Time: 112 Source-Version: 6.3.1+dfsg-1 Space: 16308 Status: successful Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-07-01T18:18:33Z Build needed 00:01:52, 16308k disk space