sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Sun, 04 Aug 2024 23:06:24 +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-93d9db45-f77a-4541-a384-419a45dd89a6' 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-sfOyIJ/resolver-nhsDDU' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [198 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [23.4 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [23.4 kB] Get:5 http://localhost:3142/debian sid InRelease [198 kB] Ign:5 http://localhost:3142/debian sid InRelease Get:5 http://localhost:3142/debian sid InRelease [198 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [21.8 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-08-04-2007.15-F-2024-08-04-2007.15.pdiff [21.8 kB] Fetched 569 kB in 7s (81.0 kB/s) 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-sfOyIJ/proteinortho-6.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/proteinortho-sfOyIJ' 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 (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 fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libicu72 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib 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 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 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 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libicu72 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib 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, 59 newly installed, 0 to remove and 0 not upgraded. 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amd64 diamond-aligner amd64 2.1.9-1 [2548 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-1 [837 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-5 [148 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-3 [3539 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 ncbi-blast+ amd64 2.16.0+ds-4 [15.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.3 MB in 0s (116 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. 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Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up ncbi-data (6.1.20170106+dfsg2-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-1) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.16) ... Setting up libuv1t64:amd64 (1.48.0-5) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up diamond-aligner (2.1.9-1) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Aug 4 23:06:42 UTC 2024. Universal Time is now: Sun Aug 4 23:06:42 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.35.1-1) ... 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 libgfortran5:amd64 (14.2.0-1) ... Setting up autoconf (2.71-3) ... 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) ... 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 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 libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up libtool (2.4.7-7) ... Setting up python3.12 (3.12.4-3) ... 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 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 libpython3-stdlib:amd64 (3.12.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.12.4-1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up ncbi-blast+ (2.16.0+ds-4) ... Setting up debhelper (13.16) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | 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_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 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(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 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/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-93d9db45-f77a-4541-a384-419a45dd89a6 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 = CXX = g++ Creating build directory ... 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 2024-08-04T23:08:08Z 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 bf9bdcd63a862c68c4429587b7b8546a32875961 1980380 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 0f1840f6bcef535c123dac9ee39ede7996a48078 6323 proteinortho_6.3.1+dfsg-1_amd64.buildinfo b5141e224cb3c1c7a41665327dbcd602dabd73f5 364052 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 7514d56a223b7f077bb7bc193226b598fd0043b8ab20d670c0e12ff6170db9cd 1980380 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 29d8023ea522202480a3cd019dcd3dabbc3ae738a8befd266073f9477aecc8df 6323 proteinortho_6.3.1+dfsg-1_amd64.buildinfo 4ded6e6b0dd8e52ab45f3fad98d9c37dbcb21360e26c813306ef5520765c6b05 364052 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 a4020c1c26263665b60b48c24177439f 1980380 debug optional proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb f81f6f065b49ddf25ee499c78b185cc1 6323 science optional proteinortho_6.3.1+dfsg-1_amd64.buildinfo 6600f9e96d70c6a773b8b354a90f9b4e 364052 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 a4020c1c26263665b60b48c24177439f 1980380 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 6600f9e96d70c6a773b8b354a90f9b4e 364052 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha1: b9f9d30d0130b3c262a0d767e4d5320bd67ddba1 1253 proteinortho_6.3.1+dfsg-1.dsc bf9bdcd63a862c68c4429587b7b8546a32875961 1980380 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb b5141e224cb3c1c7a41665327dbcd602dabd73f5 364052 proteinortho_6.3.1+dfsg-1_amd64.deb Checksums-Sha256: 264c5e85f99730d28128c7fdff728f16b79a73f3cd83374c108c17501250ee3b 1253 proteinortho_6.3.1+dfsg-1.dsc 7514d56a223b7f077bb7bc193226b598fd0043b8ab20d670c0e12ff6170db9cd 1980380 proteinortho-dbgsym_6.3.1+dfsg-1_amd64.deb 4ded6e6b0dd8e52ab45f3fad98d9c37dbcb21360e26c813306ef5520765c6b05 364052 proteinortho_6.3.1+dfsg-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 04 Aug 2024 23:08:08 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), 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 (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), 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 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexpat1 (= 2.6.2-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgfortran5 (= 14.2.0-1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), liblapack-dev (= 3.12.0-3), liblapack3 (= 3.12.0-3), liblmdb0 (= 0.9.31-1+b1), liblsan0 (= 14.2.0-1), 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 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncursesw6 (= 6.5-2), libnghttp2-14 (= 1.62.1-2), 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 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libproc2-0 (= 2:4.0.4-5), libpython3-stdlib (= 3.12.4-1), libpython3.12-minimal (= 3.12.4-3), libpython3.12-stdlib (= 3.12.4-3), libquadmath0 (= 14.2.0-1), libreadline8t64 (= 8.2-4), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libsqlite3-0 (= 3.46.0-1), libssl3t64 (= 3.3.1-2), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libuv1t64 (= 1.48.0-5), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), media-types (= 10.1.0), ncbi-blast+ (= 2.16.0+ds-4), ncbi-data (= 6.1.20170106+dfsg2-3), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-5), python3 (= 3.12.4-1), python3-minimal (= 3.12.4-1), python3.12 (= 3.12.4-3), python3.12-minimal (= 3.12.4-3), readline-common (= 8.2-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-1), 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 1980380 bytes: control archive=696 bytes. 483 bytes, 12 lines control 407 bytes, 4 lines md5sums Package: proteinortho-dbgsym Source: proteinortho Version: 6.3.1+dfsg-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2037 Depends: proteinortho (= 6.3.1+dfsg-1) Section: debug Priority: optional Description: debug symbols for proteinortho Build-Ids: 0d8075468e718170f6dee7939b25aeac1b453868 49b6c2f11d02a2c4528558e4bf8fc5d260f944bd 4bee09efed7e8404dec1a65babbe47c0d8b0e0e7 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/0d/ -rw-r--r-- root/root 1786080 2024-01-12 05:50 ./usr/lib/debug/.build-id/0d/8075468e718170f6dee7939b25aeac1b453868.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/49/ -rw-r--r-- root/root 143208 2024-01-12 05:50 ./usr/lib/debug/.build-id/49/b6c2f11d02a2c4528558e4bf8fc5d260f944bd.debug drwxr-xr-x root/root 0 2024-01-12 05:50 ./usr/lib/debug/.build-id/4b/ -rw-r--r-- root/root 118352 2024-01-12 05:50 ./usr/lib/debug/.build-id/4b/ee09efed7e8404dec1a65babbe47c0d8b0e0e7.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 22504 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 364052 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: 84 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 10 Job: /srv/debomatic/incoming/proteinortho_6.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: proteinortho Package-Time: 104 Source-Version: 6.3.1+dfsg-1 Space: 16280 Status: successful Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2024-08-04T23:08:08Z Build needed 00:01:44, 16280k disk space