sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Mon, 16 Sep 2024 14:19:27 +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: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-4e571c05-d16d-41d1-b615-8806af406a80' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /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: NOTICE: Log filtering will replace 'build/proteinortho-Bo4qtK/resolver-rlaW4d' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/proteinortho-Bo4qtK/proteinortho-6.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-Bo4qtK' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ 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, fakeroot Filtered Build-Depends: debhelper-compat (= 13), ncbi-blast+, liblapack-dev, diamond-aligner (>= 2.0.10~), procps, debhelper, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [729 B] Get:5 copy:/<>/apt_archive ./ Packages [726 B] Fetched 2064 B in 0s (188 kB/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 fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libcom-err2 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libnghttp2-14 libnsl2 libpipeline1 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libtirpc-common libtirpc3t64 libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data netbase po-debconf procps python3 python3-minimal python3.12 python3.12-minimal sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff liblapack-doc krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.12-venv python3.12-doc binfmt-support Recommended packages: med-config curl | wget | lynx libarchive-cpio-perl krb5-locales 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 fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libcom-err2 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libnghttp2-14 libnsl2 libpipeline1 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libtirpc-common libtirpc3t64 libtool libuchardet0 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data netbase po-debconf procps python3 python3-minimal python3.12 python3.12-minimal sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. 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1.36-1 [29.1 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-5 [837 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-6 [148 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-4 [3540 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.2 MB in 0s (136 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. 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Universal Time is now: Mon Sep 16 14:19:49 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... 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 (2:4.0.4-5) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-5) ... 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+b1) ... Setting up procps (2:4.0.4-5) ... 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. Setting up netbase (6.4) ... 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 libkrb5-3:amd64 (1.21.3-3) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libblas-dev:amd64 (3.12.0-3) ... 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 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 (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... 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 (0.22.5-2) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... 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 libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... 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 libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up ncbi-blast+ (2.16.0+ds-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-5 gcc-13_13.3.0-6 gcc-14_14.2.0-5 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-5 cpp-14-x86-64-linux-gnu_14.2.0-5 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diamond-aligner_2.1.9-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-5 g++-14-x86-64-linux-gnu_14.2.0-5 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-5 gcc-14-base_14.2.0-5 gcc-14-x86-64-linux-gnu_14.2.0-5 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-5 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-5 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-4 libblas-dev_3.12.0-3 libblas3_3.12.0-3 libblkid1_2.40.2-8 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-5 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libexpat1_2.6.3-1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-5 libgcc-s1_14.2.0-5 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-5 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-5 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhwasan0_14.2.0-5 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-5 libjansson4_2.14-2+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 liblapack-dev_3.12.0-3 liblapack3_3.12.0-3 libldap-2.5-0_2.5.18+dfsg-3+b1 liblmdb0_0.9.31-1+b1 liblsan0_14.2.0-5 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmbedcrypto7t64_2.28.8-1 libmbedtls14t64_2.28.8-1 libmbedx509-1t64_2.28.8-1 libmd0_1.1.0-2 libmount1_2.40.2-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ 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 /<> 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 | +------------------------------------------------------------------------------+ /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=/<> 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-4e571c05-d16d-41d1-b615-8806af406a80 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -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 '/<>' 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 '/<>' 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 '/<>' CC = cc CCFLAGS = Creating build directory ... CXX = g++ CXXFLAGS = -g -O2 -ffile-prefix-map=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -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 '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/<>' [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 '/<>' rm test_* remove.* test/C_clean.faa make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p /<>/debian/proteinortho/usr/bin dh_auto_install -- install PREFIX=/<>/debian/proteinortho/usr/bin make -j2 install DESTDIR=/<>/proteinortho-6.3.1\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install PREFIX=/<>/proteinortho-6.3.1\+dfsg/debian/proteinortho/usr/bin make[2]: Entering directory '/<>' INSTALLING everything to /<>/debian/proteinortho/usr/bin 'proteinortho6.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho6.pl' 'proteinortho' -> '/<>/debian/proteinortho/usr/bin/proteinortho' 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_extract_from_graph.pl' 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_formatUsearch.pl' 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_compareProteinorthoGraphs.pl' 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_do_mcl.pl' 'src/BUILD/Linux_x86_64/proteinortho2html.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho2html.pl' 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho2xml.pl' 'src/BUILD/Linux_x86_64/proteinortho_clustering' -> '/<>/debian/proteinortho/usr/bin/proteinortho_clustering' 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_singletons.pl' 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' -> '/<>/debian/proteinortho/usr/bin/proteinortho_ffadj_mcs.py' 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho2tree.pl' 'src/BUILD/Linux_x86_64/proteinortho_history.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_history.pl' 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' -> '/<>/debian/proteinortho/usr/bin/proteinortho_cleanupblastgraph' 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' -> '/<>/debian/proteinortho/usr/bin/proteinortho_graphMinusRemovegraph' 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_grab_proteins.pl' 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' -> '/<>/debian/proteinortho/usr/bin/proteinortho_summary.pl' Everything installed successfully to /<>/debian/proteinortho/usr/bin. If needed you can add /<>/debian/proteinortho/usr/bin to $PATH with 'export PATH=$PATH:/<>/debian/proteinortho/usr/bin'. make[2]: Nothing to be done for 'install'. make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' 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 '/<>' dh_fixperms find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' 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 2024-09-16T14:21:59Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ 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 a63aec3f08287f1a69b0f3571506851bbc2365a9 1979936 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb f3f2906b8a58a2e64f50ab2adccce1271c7f0476 6537 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 39d6aa6c67ebc98b784e2c4c0f51b954acd208e1 364152 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 d06c43240e81c06dd8d9f581582a65099e8e5cbc40de6e063264ad89241df021 1979936 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 7558057326a588b8bd579fdfe332c8d19f247b7635ad307ff9cb2753f8822974 6537 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 4ab16acc7cf8ce1b88b16e2dc656cdcbb18104481a965399fa2a95d8656ed250 364152 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 f5a396d38f885cb71ee39e600a1d5a2d 1979936 debug optional proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 358e414a13ecc5596b4ea9841609eaf5 6537 science optional proteinortho_6.3.1+dfsg-1_amd64.buildinfo e7afc70075284ba8164b56f27e1d72bd 364152 science optional proteinortho_6.3.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ 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 f5a396d38f885cb71ee39e600a1d5a2d 1979936 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb e7afc70075284ba8164b56f27e1d72bd 364152 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha1: b9f9d30d0130b3c262a0d767e4d5320bd67ddba1 1253 proteinortho_6.3.1+dfsg-1.dsc a63aec3f08287f1a69b0f3571506851bbc2365a9 1979936 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 39d6aa6c67ebc98b784e2c4c0f51b954acd208e1 364152 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 264c5e85f99730d28128c7fdff728f16b79a73f3cd83374c108c17501250ee3b 1253 proteinortho_6.3.1+dfsg-1.dsc d06c43240e81c06dd8d9f581582a65099e8e5cbc40de6e063264ad89241df021 1979936 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 4ab16acc7cf8ce1b88b16e2dc656cdcbb18104481a965399fa2a95d8656ed250 364152 proteinortho_6.3.1+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 16 Sep 2024 14:21:58 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-5), cpp-14-x86-64-linux-gnu (= 14.2.0-5), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diamond-aligner (= 2.1.9-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-5), g++-14-x86-64-linux-gnu (= 14.2.0-5), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-5), gcc-14-base (= 14.2.0-5), gcc-14-x86-64-linux-gnu (= 14.2.0-5), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-5), libatomic1 (= 14.2.0-5), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43.1-4), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.2-8), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-5), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexpat1 (= 2.6.3-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-5), libgcc-s1 (= 14.2.0-5), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-5), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-5), libgprofng0 (= 2.43.1-4), libgssapi-krb5-2 (= 1.21.3-3), libhwasan0 (= 14.2.0-5), libicu72 (= 72.1-5), libisl23 (= 0.27-1), libitm1 (= 14.2.0-5), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), liblapack-dev (= 3.12.0-3), liblapack3 (= 3.12.0-3), liblmdb0 (= 0.9.31-1+b1), liblsan0 (= 14.2.0-5), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmbedcrypto7t64 (= 2.28.8-1), libmbedtls14t64 (= 2.28.8-1), libmbedx509-1t64 (= 2.28.8-1), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncursesw6 (= 6.5-2), libnghttp2-14 (= 1.63.0-1), libnsl2 (= 1.3.0-3+b2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libproc2-0 (= 2:4.0.4-5), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-5), libreadline8t64 (= 8.2-5), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libsqlite3-0 (= 3.46.1-1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-5), libstdc++6 (= 14.2.0-5), libsystemd0 (= 256.6-1), libtinfo6 (= 6.5-2), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-5), libubsan1 (= 14.2.0-5), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libuv1t64 (= 1.48.0-6), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), ncbi-blast+ (= 2.16.0+ds-6), ncbi-data (= 6.1.20170106+dfsg2-4), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-5), python3 (= 3.12.5-1+b1), python3-minimal (= 3.12.5-1+b1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.10-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-8), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) 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 | +------------------------------------------------------------------------------+ proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 1979936 bytes: control archive=700 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: 2037 Depends: proteinortho (= 6.3.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for proteinortho Build-Ids: 1b86ee96769aacb1668d7fbbad24ce5540481f2b 971810cf0aa651edccc1160b96cd4be2cde4960c a16958abb2a3c2f9450845f463c0fc0448d5d2f6 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/1b/ -rw-r--r-- root/root 143216 2024-01-12 05:50 ./usr/lib/debug/.build-id/1b/86ee96769aacb1668d7fbbad24ce5540481f2b.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/97/ -rw-r--r-- root/root 118360 2024-01-12 05:50 ./usr/lib/debug/.build-id/97/1810cf0aa651edccc1160b96cd4be2cde4960c.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/a1/ -rw-r--r-- root/root 1786048 2024-01-12 05:50 ./usr/lib/debug/.build-id/a1/6958abb2a3c2f9450845f463c0fc0448d5d2f6.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 22512 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 364152 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 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 16280 Build-Time: 127 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 15 Job: /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: proteinortho Package-Time: 152 Source-Version: 6.3.1+dfsg-1 Space: 16280 Status: successful Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-09-16T14:21:59Z Build needed 00:02:32, 16280k disk space