sbuild (Debian sbuild) 0.88.2 (16 January 2025) on carme.larted.org.uk +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Wed, 22 Jan 2025 09:39:29 +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 Wed, 22 Jan 2025 09:39:31 +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 Wed, 22 Jan 2025 09:39:31 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:2 http://deb.debian.org/debian unstable InRelease [205 kB] Get:1 file:/srv/reprepro perl-5.40 InRelease [3030 B] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 file:/srv/reprepro perl-5.40/main amd64 Packages [8875 B] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [144 kB] Get:6 http://localhost:3142/debian sid InRelease [205 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2025-01-22-0806.21-F-2025-01-20-0805.29.pdiff [147 kB] Fetched 829 kB in 7s (126 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2494 kB of archives. After this operation, 4096 B disk space will be freed. Get:1 http://deb.debian.org/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.24 [1114 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 apt amd64 2.9.24 [1380 kB] Fetched 2494 kB in 0s (65.8 MB/s) (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 ... 23043 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.24_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.24) over (2.9.23) ... Setting up libapt-pkg6.0t64:amd64 (2.9.24) ... (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 ... 23043 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.24_amd64.deb ... Unpacking apt (2.9.24) over (2.9.23) ... Setting up apt (2.9.24) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Fetch source files Wed, 22 Jan 2025 09:39:42 +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 Wed, 22 Jan 2025 09:39:42 +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-jg7xq7/resolver-6wBwBB/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/apt_archive ./ InRelease Get:2 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/apt_archive ./ Release [609 B] Ign:3 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/apt_archive ./ Release.gpg Get:4 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/apt_archive ./ Sources [712 B] Get:5 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/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 libicu72 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 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 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 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 libicu72 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 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 netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 58.2 MB of archives. After this operation, 248 MB of additional disk space will be used. Get:1 copy:/build/proteinortho-jg7xq7/resolver-6wBwBB/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [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 1.23.0-7 [1185 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 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 2.13.0-1 [1420 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [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 1.14.1-1 [19.6 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 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 libicu72 amd64 72.1-6 [9421 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 diamond-aligner amd64 2.1.9-1 [2548 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Preconfiguring packages ... Fetched 58.2 MB in 0s (193 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... 23043 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.1-3_amd64.deb ... Unpacking python3.13-minimal (3.13.1-3) ... Setting up libpython3.13-minimal:amd64 (3.13.1-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.1-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 23377 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... 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Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up libicu72:amd64 (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up diamond-aligner (2.1.9-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 22 09:39:50 UTC 2025. Universal Time is now: Wed Jan 22 09:39:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up autopoint (0.23.1-1) ... Setting up libgfortran5:amd64 (14.2.0-14) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up netbase (6.4) ... 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 (3.6.2-3) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libblas-dev:amd64 (3.12.0-4) ... 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 (3.13.1-2) ... 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 (1.14.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 (0.23.1-1) ... Setting up libtool (2.5.4-2) ... Setting up python3.13 (3.13.1-3) ... Setting up python3 (3.13.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.2-3) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... 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 (3.6.2-3) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up debhelper (13.24.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-5) ... +------------------------------------------------------------------------------+ | Check architectures Wed, 22 Jan 2025 09:39:51 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Wed, 22 Jan 2025 09:39:51 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.11.10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1 (2024-11-23) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20250108-1 dpkg-dev_1.22.14 g++-13_13.3.0-12 g++-14_14.2.0-14 gcc-13_13.3.0-12 gcc-14_14.2.0-14 libc6-dev_2.40-5 libstdc++-13-dev_13.3.0-12 libstdc++-14-dev_14.2.0-14 libstdc++6_14.2.0-14 linux-libc-dev_6.12.10-1 Package versions: adduser_3.137 apt_2.9.24 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20250108-1 binutils-common_2.43.50.20250108-1 binutils-x86-64-linux-gnu_2.43.50.20250108-1 bsdextrautils_2.40.4-1 bsdutils_1:2.40.4-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-13_13.3.0-12 cpp-13-x86-64-linux-gnu_13.3.0-12 cpp-14_14.2.0-14 cpp-14-x86-64-linux-gnu_14.2.0-14 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-11 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-1 diamond-aligner_2.1.9-1 diffutils_1:3.10-2 dirmngr_2.2.46-1+b1 dpkg_1.22.14 dpkg-dev_1.22.14 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.3.0-12 g++-13-x86-64-linux-gnu_13.3.0-12 g++-14_14.2.0-14 g++-14-x86-64-linux-gnu_14.2.0-14 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.3.0-12 gcc-13-base_13.3.0-12 gcc-13-x86-64-linux-gnu_13.3.0-12 gcc-14_14.2.0-14 gcc-14-base_14.2.0-14 gcc-14-x86-64-linux-gnu_14.2.0-14 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 gnupg_2.2.46-1 gnupg-l10n_2.2.46-1 gnupg-utils_2.2.46-1+b1 gpg_2.2.46-1+b1 gpg-agent_2.2.46-1+b1 gpg-wks-client_2.2.46-1+b1 gpgconf_2.2.46-1+b1 gpgsm_2.2.46-1+b1 gpgv_2.2.46-1+b1 grep_3.11-4 groff-base_1.23.0-7 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_2.9.24 libarchive-zip-perl_1.68-1 libasan8_14.2.0-14 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-14 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.43.50.20250108-1 libblas-dev_3.12.0-4 libblas3_3.12.0-4 libblkid1_2.40.4-1 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc-l10n_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-14 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.43.50.20250108-1 libctf0_2.43.50.20250108-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.14 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libexpat1_2.6.4-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.1-1 libgcc-13-dev_13.3.0-12 libgcc-14-dev_14.2.0-14 libgcc-s1_14.2.0-14 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-14 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-14 libgpg-error0_1.51-3 libgprofng0_2.43.50.20250108-1 libhogweed6t64_3.10-1+b1 libhwasan0_14.2.0-14 libicu72_72.1-6 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-14 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblapack-dev_3.12.0-4 liblapack3_3.12.0-4 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.9+dfsg-1 liblmdb0_0.9.31-1+b2 liblsan0_14.2.0-14 liblz4-1_1.9.4-4 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmbedcrypto16_3.6.2-3 libmbedtls21_3.6.2-3 libmbedx509-7_3.6.2-3 libmd0_1.1.0-2+b1 libmount1_2.40.4-1 libmpc3_1.3.1-1+b3 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libuuid1_2.40.4-1 libuv1t64_1.48.0-7 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxxhash0_0.8.3-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.10-1 locales-all_2.40-5 login_1:4.16.0-2+really2.40.4-1 login.defs_1:4.16.0-7 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 ncbi-blast+_2.16.0+ds-6+b1 ncbi-data_6.1.20170106+dfsg2-5 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.1-1 perl-base_5.40.1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-1 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 python3_3.13.1-2 python3-minimal_3.13.1-2 python3.13_3.13.1-3 python3.13-minimal_3.13.1-3 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sqv_1.2.1-5 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-1 usr-is-merged_39+nmu2 util-linux_2.40.4-1 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Wed, 22 Jan 2025 09:39:51 +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 vv9nhH9YUOktpfyr2dCJinpqEQ5uv1eYeSXpyNIJzwWSPeWQW+zxuPDSa0u750br C3/8UjoMWTrVDbTc0Y9CN9coUHkghXPvLsxxpqpj4gBIWgjFM3SMNP56p1Rv5uRx QZUk5F81PteMIwgkp0z3bY0ZezA2o7eLFjGmrwLwl4l0hdWrjHyhumtJuTldFZt9 HJ6rlvfDuj+Kml2uC41CMoHV5thvnQC2MjBVQjG38IYf2AAyd6oafGFA8hHqF4qu eL69T0QQeXHICNXvCE4xyjVM8xIWfeYNCbkZULbOq7bdEzueDZEP/GzLCUkM+d2d YXWwk5h9Tsw= =8nLU -----END PGP SIGNATURE----- gpgv: Signature made Fri Jan 12 05:54:55 2024 UTC 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 ./proteinortho_6.3.1+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting proteinortho in /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg dpkg-source: info: unpacking proteinortho_6.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_6.3.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying deb_diamond Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Wed, 22 Jan 2025 09:39:52 +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-jg7xq7/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-aaf11e6c-359e-4cca-a6c2-f3edf531fa1c 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-jg7xq7/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-jg7xq7/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-jg7xq7/proteinortho-6.3.1+dfsg' CC = cc CCFLAGS = CXX = g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/build/proteinortho-jg7xq7/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 = Creating build directory ... 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-jg7xq7/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-jg7xq7/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-jg7xq7/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-jg7xq7/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/proteinortho-jg7xq7/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-jg7xq7/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/build/proteinortho-jg7xq7/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-jg7xq7/proteinortho-6.3.1+dfsg' mkdir -p /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin make -j2 install DESTDIR=/build/proteinortho-jg7xq7/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/build/proteinortho-jg7xq7/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg' INSTALLING everything to /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin. If needed you can add /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg' make[1]: Leaving directory '/build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/proteinortho-jg7xq7/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-jg7xq7/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-jg7xq7/proteinortho-6.3.1+dfsg' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/build/proteinortho-jg7xq7/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' in '../proteinortho_6.3.1+dfsg-1_amd64.deb'. dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_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 2025-01-22T09:41:24Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Wed, 22 Jan 2025 09:41:24 +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 44f884c0c67dc6d5ab0934665ae7baa49e23f94e 1983280 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 593d8370aca2f6084497ee041e1e597403b06626 6370 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 5503c7eabd4d24e883995c736079fa93b8a5126e 364136 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 b42236ba03e2f30c015051e435cffd752ba35546e2e3e8e53ecde50cb26fbf73 1983280 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb b1a25570439688905617e4679bb4c614c3e22300ce2c438ef8937786e3eb592c 6370 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 71182a2cf6802b083639db15dd077ebc71c47615ae1d42e7375226e9fec53ee5 364136 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 f003459193f0d6b67a76ecdda41dd9ef 1983280 debug optional proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 7503b8d56d5de73fa76f6af7ae8796a2 6370 science optional proteinortho_6.3.1+dfsg-1_amd64.buildinfo fcbcdc8391da0880712e0e048990c791 364136 science optional proteinortho_6.3.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Wed, 22 Jan 2025 09:41:24 +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 f003459193f0d6b67a76ecdda41dd9ef 1983280 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb fcbcdc8391da0880712e0e048990c791 364136 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha1: b9f9d30d0130b3c262a0d767e4d5320bd67ddba1 1253 proteinortho_6.3.1+dfsg-1.dsc 44f884c0c67dc6d5ab0934665ae7baa49e23f94e 1983280 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 5503c7eabd4d24e883995c736079fa93b8a5126e 364136 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 264c5e85f99730d28128c7fdff728f16b79a73f3cd83374c108c17501250ee3b 1253 proteinortho_6.3.1+dfsg-1.dsc b42236ba03e2f30c015051e435cffd752ba35546e2e3e8e53ecde50cb26fbf73 1983280 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 71182a2cf6802b083639db15dd077ebc71c47615ae1d42e7375226e9fec53ee5 364136 proteinortho_6.3.1+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 22 Jan 2025 09:41:24 +0000 Build-Path: /build/proteinortho-jg7xq7/proteinortho-6.3.1+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.23.1-1), autotools-dev (= 20220109.1), base-files (= 13.6), base-passwd (= 3.6.6), bash (= 5.2.37-1), binutils (= 2.43.50.20250108-1), binutils-common (= 2.43.50.20250108-1), binutils-x86-64-linux-gnu (= 2.43.50.20250108-1), bsdextrautils (= 2.40.4-1), bsdutils (= 1:2.40.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.5-1+b1), cpp (= 4:14.2.0-1), cpp-13 (= 13.3.0-12), cpp-13-x86-64-linux-gnu (= 13.3.0-12), cpp-14 (= 14.2.0-14), cpp-14-x86-64-linux-gnu (= 14.2.0-14), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-11), debconf (= 1.5.89), debhelper (= 13.24.1), debianutils (= 5.21), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-1), diamond-aligner (= 2.1.9-1), diffutils (= 1:3.10-2), dpkg (= 1.22.14), dpkg-dev (= 1.22.14), dwz (= 0.15-1+b1), file (= 1:5.45-3+b1), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-14), g++-14-x86-64-linux-gnu (= 14.2.0-14), 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LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1705038622" +------------------------------------------------------------------------------+ | Package contents Wed, 22 Jan 2025 09:41:24 +0000 | +------------------------------------------------------------------------------+ proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 1983280 bytes: control archive=704 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: 2107 Depends: proteinortho (= 6.3.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for proteinortho Build-Ids: bc8ad19b6c79e1989a18ea28edfa17d6159f2044 d9006d578bb2ef28ff61b8a289ddfccd736184ee da04392f239592c557bdb168eb7647bfd8b4fb6c drwxr-xr-x root/root 0 2024-01-12 05:50 ./ drwxr-xr-x 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./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 364136 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 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-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 Wed, 22 Jan 2025 09:41:25 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Wed, 22 Jan 2025 09:41:25 +0000 | +------------------------------------------------------------------------------+ Purging /build/proteinortho-jg7xq7 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Wed, 22 Jan 2025 09:41:25 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 16304 Build-Time: 92 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 9 Job: /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: proteinortho Package-Time: 115 Source-Version: 6.3.1+dfsg-1 Space: 16304 Status: successful Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-01-22T09:41:24Z Build needed 00:01:55, 16304k disk space