DC-Build-Header: proteinortho 6.3.1+dfsg-1 / 2025-05-01 13:18:15 +0000 DC-Task: type:rebuild-full source:proteinortho version:6.3.1+dfsg-1 chroot:unstable esttime:156 logfile:/tmp/proteinortho_6.3.1+dfsg-1_unstable_reverse.log modes:shuffle-reverse DC-System-Info: 8 cores (Intel(R) Xeon(R) Platinum 8175M CPU @ 2.50GHz), 32516492 kB RAM DC-Sbuild-call: su user42 -c 'SBUILD_CONFIG=/tmp/sbuildcfg.69oRNd sbuild -n -A -s --force-orig-source --apt-update -d unstable -v --no-run-lintian proteinortho_6.3.1+dfsg-1' sbuild (Debian sbuild) 0.88.4~bpo12+2 (24 February 2025) on ip-10-84-234-80 +==============================================================================+ | proteinortho 6.3.1+dfsg-1 (amd64) Thu, 01 May 2025 13:18:15 +0000 | +==============================================================================+ Package: proteinortho Version: 6.3.1+dfsg-1 Source Version: 6.3.1+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Unpacking /home/user42/.cache/sbuild/unstable-amd64.tar.gz to /tmp/tmp.sbuild.6AzbOkDxdN... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 01 May 2025 13:18:23 +0000 | +------------------------------------------------------------------------------+ Hit:1 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Thu, 01 May 2025 13:18:25 +0000 | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/proteinortho.git Please use: git clone https://salsa.debian.org/med-team/proteinortho.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 385 kB of source archives. Get:1 http://deb.debian.org/debian sid/main proteinortho 6.3.1+dfsg-1 (dsc) [2161 B] Get:2 http://deb.debian.org/debian sid/main proteinortho 6.3.1+dfsg-1 (tar) [376 kB] Get:3 http://deb.debian.org/debian sid/main proteinortho 6.3.1+dfsg-1 (diff) [7248 B] Fetched 385 kB in 0s (9952 kB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 01 May 2025 13:18:25 +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/reproducible-path/resolver-ZgZfvS/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-ZgZfvS/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-ZgZfvS/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-ZgZfvS/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-ZgZfvS/apt_archive ./ Sources [712 B] Get:5 copy:/build/reproducible-path/resolver-ZgZfvS/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... 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 libffi8 libfile-stripnondeterminism-perl libgfortran5 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libtool libuchardet0 libunistring5 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff liblapack-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support readline-doc Recommended packages: med-config curl | wget | lynx libarchive-cpio-perl libgpm2 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 libffi8 libfile-stripnondeterminism-perl libgfortran5 liblapack-dev liblapack3 liblmdb0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncursesw6 libnghttp2-14 libpipeline1 libproc2-0 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libtool libuchardet0 libunistring5 libuv1t64 libxml2 m4 man-db media-types ncbi-blast+ ncbi-data netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 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http://deb.debian.org/debian sid/main amd64 debhelper all 13.24.2 [919 kB] Get:47 http://deb.debian.org/debian sid/main amd64 diamond-aligner amd64 2.1.11-2 [2648 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:51 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get:52 http://deb.debian.org/debian sid/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get:53 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b2 [45.2 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get:59 http://deb.debian.org/debian sid/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get:60 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.16.0+ds-6+b1 [15.2 MB] Preconfiguring packages ... Fetched 49.6 MB in 0s (137 MB/s) Selecting previously unselected package libpython3.13-minimal:amd64. (Reading database ... 12856 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.3-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.7.1-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_amd64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:amd64 (3.13.3-2) ... Setting up libexpat1:amd64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 13190 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_amd64.deb ... Unpacking python3-minimal (3.13.3-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_amd64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up liblmdb0:amd64 (0.9.31-1+b2) ... Setting up ncbi-data (6.1.20170106+dfsg2-5) ... Setting up bsdextrautils (2.41-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up diamond-aligner (2.1.11-2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libproc2-0:amd64 (2:4.0.4-8) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up netbase (6.5) ... Setting up libmbedcrypto16:amd64 (3.6.3-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:amd64 (3.6.3-1) ... Setting up liblapack-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libmbedtls21:amd64 (3.6.3-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:amd64 (3.13.3-2) ... Setting up libpython3-stdlib:amd64 (3.13.3-1) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... 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 (13.24.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-7) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 01 May 2025 13:18:42 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Thu, 01 May 2025 13:18:42 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-32-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.18 g++-14_14.2.0-19 gcc-14_14.2.0-19 libc6-dev_2.41-7 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.25-1 Package versions: apt_3.0.1 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.7 base-passwd_3.6.7 bash_5.2.37-2 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-4 bsdutils_1:2.41-4 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-2 cpp_4:14.2.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.22 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diamond-aligner_2.1.11-2 diffutils_1:3.10-4 dpkg_1.22.18 dpkg-dev_1.22.18 dwz_0.15-1+b1 fakeroot_1.37.1.1-1 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 grep_3.11-4 groff-base_1.23.0-7 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-pkg7.0_3.0.1 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblas-dev_3.12.1-2 libblas3_3.12.1-2 libblkid1_2.41-4 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-7 libc-dev-bin_2.41-7 libc6_2.41-7 libc6-dev_2.41-7 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-7 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.278 libdebhelper-perl_13.24.2 libdpkg-perl_1.22.18 libelf1t64_0.192-4 libexpat1_2.7.1-1 libfakeroot_1.37.1.1-1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-19 libgmp10_2:6.3.0+dfsg-3 libgomp1_14.2.0-19 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-19 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 liblapack-dev_3.12.1-2 liblapack3_3.12.1-2 liblastlog2-2_2.41-4 liblmdb0_0.9.31-1+b2 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmbedcrypto16_3.6.3-1 libmbedtls21_3.6.3-1 libmbedx509-7_3.6.3-1 libmd0_1.1.0-2+b1 libmount1_2.41-4 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libpam-modules_1.7.0-3 libpam-modules-bin_1.7.0-3 libpam-runtime_1.7.0-3 libpam0g_1.7.0-3 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-3 libpipeline1_1.5.8-1 libproc2-0_2:4.0.4-8 libpython3-stdlib_3.13.3-1 libpython3.13-minimal_3.13.3-2 libpython3.13-stdlib_3.13.3-2 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-4 libsqlite3-0_3.46.1-3 libssl3t64_3.5.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.5-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.5-2 libunistring5_1.3-2 libuuid1_2.41-4 libuv1t64_1.50.0-2 libxml2_2.12.7+dfsg+really2.9.14-0.4 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.25-1 login_1:4.16.0-2+really2.41-4 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.0-1 mawk_1.3.4.20250131-1 media-types_13.0.0 mount_2.41-4 ncbi-blast+_2.16.0+ds-6+b1 ncbi-data_6.1.20170106+dfsg2-5 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 netbase_6.5 openssl-provider-legacy_3.5.0-1 passwd_1:4.17.4-2 patch_2.8-1 perl_5.40.1-3 perl-base_5.40.1-3 perl-modules-5.40_5.40.1-3 po-debconf_1.0.21+nmu1 procps_2:4.0.4-8 python3_3.13.3-1 python3-minimal_3.13.3-1 python3.13_3.13.3-2 python3.13-minimal_3.13.3-2 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_0.0.25 sqv_1.3.0-1 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 tzdata_2025b-2 util-linux_2.41-4 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Thu, 01 May 2025 13:18:42 +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: 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PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -sa 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 --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean debian/rules:10: update target 'clean' due to: target does not exist dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' Makefile:485: update target 'clean' due to: target is .PHONY 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/reproducible-path/proteinortho-6.3.1+dfsg' dh_clean dpkg-source -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 debian/rules:10: update target 'binary' due to: target does not exist dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' Makefile:242: update target 'src/BUILD/Linux_x86_64/proteinortho_cleanupblastgraph' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi Creating build directory ... echo "[ 50%] Building **cleanupblastgraph**" [ 50%] Building **cleanupblastgraph** echo "g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 " && g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 Makefile:253: update target 'src/BUILD/Linux_x86_64/proteinortho_graphMinusRemovegraph' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi echo "[ 25%] Building **graphMinusRemovegraph**" [ 25%] Building **graphMinusRemovegraph** echo "g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 " && g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 Makefile:151: update target 'src/BUILD/Linux_x86_64/proteinortho_history.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_history.pl src/BUILD/Linux_x86_64/proteinortho_history.pl Makefile:182: update target 'src/BUILD/Linux_x86_64/proteinortho_clustering' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi echo "[ 10%] Prepare proteinortho_clustering ..." [ 10%] Prepare proteinortho_clustering ... echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; [ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking) echo "g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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" && g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 && ([ $? -eq 0 ] && src/BUILD/Linux_x86_64/proteinortho_clustering -test && [ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \ echo "......dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX)."; \ echo "g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -lpthread" && g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -lpthread && ([ $? -eq 0 ] && src/BUILD/Linux_x86_64/proteinortho_clustering -test && [ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \ echo "......dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas."; \ echo "g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -lopenblas -pthread -lpthread" && g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -lopenblas -pthread -lpthread && ([ $? -eq 0 ] && src/BUILD/Linux_x86_64/proteinortho_clustering -test && [ $? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \ echo "......last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking."; \ echo "......[ 33%] Extracting the LAPACK library"; \ if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \ echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \ if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo "mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=g++ > /dev/null; make all -j4"; mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=g++ > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \ echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \ echo "g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas -Wl,-z,relro -Wl,-z,now -lgfortran" && g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas -Wl,-z,relro -Wl,-z,now -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) g++ -std=c++11 -O3 -funroll-loops -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/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 Makefile:147: update target 'src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_ffadj_mcs.py src/BUILD/Linux_x86_64/proteinortho_ffadj_mcs.py Makefile:155: update target 'src/BUILD/Linux_x86_64/proteinortho_summary.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_summary.pl src/BUILD/Linux_x86_64/proteinortho_summary.pl Makefile:139: update target 'src/BUILD/Linux_x86_64/proteinortho_singletons.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_singletons.pl src/BUILD/Linux_x86_64/proteinortho_singletons.pl Makefile:135: update target 'src/BUILD/Linux_x86_64/proteinortho2xml.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho2xml.pl src/BUILD/Linux_x86_64/proteinortho2xml.pl Makefile:131: update target 'src/BUILD/Linux_x86_64/proteinortho2html.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho2html.pl src/BUILD/Linux_x86_64/proteinortho2html.pl Makefile:143: update target 'src/BUILD/Linux_x86_64/proteinortho2tree.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho2tree.pl src/BUILD/Linux_x86_64/proteinortho2tree.pl Makefile:123: update target 'src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_do_mcl.pl src/BUILD/Linux_x86_64/proteinortho_do_mcl.pl Makefile:127: update target 'src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_formatUsearch.pl src/BUILD/Linux_x86_64/proteinortho_formatUsearch.pl Makefile:119: update target 'src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_grab_proteins.pl src/BUILD/Linux_x86_64/proteinortho_grab_proteins.pl Makefile:115: update target 'src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi cp src/proteinortho_compareProteinorthoGraphs.pl src/BUILD/Linux_x86_64/proteinortho_compareProteinorthoGraphs.pl Makefile:111: update target 'src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl' due to: target does not exist if [ ! -d src/BUILD/Linux_x86_64 ]; then echo "Creating build directory ..."; mkdir -p src/BUILD/Linux_x86_64; fi Makefile:159: update target 'echoENV' due to: target does not exist echo -n "CC = " cp src/proteinortho_extract_from_graph.pl src/BUILD/Linux_x86_64/proteinortho_extract_from_graph.pl CC = echo cc cc echo -n "CCFLAGS = " CCFLAGS = echo echo -n "CXX = " CXX = echo g++ g++ echo -n "CXXFLAGS = " CXXFLAGS = echo -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -ffile-prefix-map=/build/reproducible-path/proteinortho-6.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection echo -n "MTUNEARCHFLAGS = " MTUNEARCHFLAGS = echo echo -n "LDFLAGS = " LDFLAGS = echo -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now echo -n "LDLIBS = " LDLIBS = echo echo -n "STATIC = " STATIC = echo FALSE FALSE - 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! if [ ! -e src/BUILD/Linux_x86_64/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi Makefile:108: update target 'all' due to: target is .PHONY echo "[100%] Everything is compiled with no errors." [100%] Everything is compiled with no errors. make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' debian/rules:14: update target 'override_dh_auto_test' due to: target does not exist dh_auto_test --no-parallel make -j1 test make[2]: Entering directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' Makefile:436: update target 'test_integrity_2' due to: target is .PHONY ./proteinortho6.pl -silent -force -singles -project=test_singles_diamond -p=diamond test/*.faa 2>/dev/null; echo -n "testing if all proteins are in the output (using -singles): "; testing if all proteins are in the output (using -singles): grep -E '^>' test/C.faa test/C2.faa test/E.faa test/L.faa test/M.faa | wc -l | sed -E 's/[ \t]//g' > test_singles_diamond.true; perl -le 'my %d; while(<>){if(/^#/){next;}$_=~s/^[^\t]+\t[^\t]+\t[^\t]+//g;chomp;my $j=0;my $l=join ",", map {$j+=1;"$j:$_"} split /\t/,$_;foreach my $i (split /,/,$l){if($i !~ /:[*]/ && $i ne ""){$d{$i}=1;}}}print scalar keys %d' test_singles_diamond.proteinortho.tsv | sed -E 's/[ \t]//g' > test_singles_diamond.test; set -e ; diff test_singles_diamond.true test_singles_diamond.test; echo "passed" passed Makefile:429: update target 'test_integrity' due to: target is .PHONY ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa 2>/dev/null; echo -n "testing if there is a protein that occurs twice in the output: "; testing if there is a protein that occurs twice in the output: perl -e 'my %d; while(<>){$_=~s/^[^\t]+\t[^\t]+\t[^\t]+//g;chomp;foreach my $i (split /[,\t]/,$_){if($i ne "*" && $i ne "" && exists $d{$i}){die "error found a protein that occurs in the output twice <${i}>\n"}$d{$i}=1;}}' test_diamond.proteinortho.tsv; echo "passed" passed Makefile:469: update target 'test_step3_K5' due to: target is .PHONY 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"; echo "passed" passed Makefile:463: update target 'test_step3_P4' due to: target is .PHONY 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"; echo "passed" passed Makefile:457: update target 'test_step3_P3_K5' due to: target is .PHONY 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"; echo "passed" passed Makefile:451: update target 'test_step3_ring4_K5_lapack' due to: target is .PHONY 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"; echo "passed" passed Makefile:445: update target 'test_step3_ring4_K5_power' due to: target is .PHONY 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"; echo "passed" passed Makefile:399: update target 'test_step3' due to: target is .PHONY ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; echo "[TEST] 2. -step=3 tests (proteinortho_clustering) " [TEST] 2. -step=3 tests (proteinortho_clustering) echo -n " [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -test> /dev/null 2>&1 [1/6] various test functions of proteinortho_clustering (if this fails, try make clean first): echo "passed" passed echo -n " [2/6] Test proteinortho_clustering using lapack: "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 -weighted 2 -double 0 -debug 1 test_blastp.blast-graph 2>test_lapack.err | sort | awk -F'\t' '{$3="";print $0}' >test_lapack.proteinortho.tsv ; \ set -e ; ./src/chk_test.pl test_lapack.proteinortho.tsv; [2/6] Test proteinortho_clustering using lapack: echo "passed" passed perl -lne 'print join "\t", sort split("\t",$_)' remove.graph | sort | uniq > remove.graph.lapack; echo -n " [3/6] Test proteinortho_clustering using power: "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 0 -weighted 2 -double 0 -debug 1 test_blastp.blast-graph 2>test_power.err | sort | awk -F'\t' '{$3="";print $0}' >test_power.proteinortho.tsv; \ set -e ; ./src/chk_test.pl test_power.proteinortho.tsv; [3/6] Test proteinortho_clustering using power: echo "passed" passed perl -lne 'print join "\t", sort split("\t",$_)' remove.graph | sort | uniq > remove.graph.power; echo -n " [4/6] Test proteinortho_clustering using lapack and no weights: "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -lapack 2 -weighted 0 -double 0 -debug 1 test_blastp.blast-graph 2>test_power.err | sort | awk -F'\t' '{$3="";print $0}' >test_power.proteinortho.tsv; \ set -e ; ./src/chk_test.pl test_power.proteinortho.tsv; [4/6] Test proteinortho_clustering using lapack and no weights: echo "passed" passed echo -n " [5/6] Test proteinortho_clustering using maxnodes/flooding: "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -maxnodes 2 -conn 0 -debug 1 test_blastp.blast-graph 2>test_power.err | sort | awk -F'\t' '{$3="";print $0}' >test_power.proteinortho.tsv; \ set -e ; ./src/chk_test.pl test_power.proteinortho.tsv; [5/6] Test proteinortho_clustering using maxnodes/flooding: echo "passed" passed echo -n " [6/6] Test proteinortho_clustering using no clustering at all: "; \ OMP_NUM_THREADS=1 src/BUILD/Linux_x86_64/proteinortho_clustering -conn -1 -debug 1 test_blastp.blast-graph 2>test_power.err | sort | awk -F'\t' '{$3="";print $0}' >test_power.proteinortho.tsv; \ set -e ; ./src/chk_test.pl test_power.proteinortho.tsv; [6/6] Test proteinortho_clustering using no clustering at all: echo "passed" passed Makefile:480: update target 'test_clean2' due to: target is .PHONY echo "[TEST] Clean up all test files..."; \ rm -rf remove.graph* proteinortho_cache_test_* test.* test_* test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*> /dev/null 2>&1; [TEST] Clean up all test files... Makefile:287: update target 'test_step2' due to: target is .PHONY echo "[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)" [TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped) echo -n " [1/12] -p=blastp test: " [1/12] -p=blastp test: if [ "/usr/bin/blastp" = "" ]; then\ echo "blastp missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_blastp -p=blastp test/*.faa; \ set -e ; ./src/chk_test.pl test_blastp.proteinortho.tsv; \ echo "passed"; \ fi passed echo -n " [2/12] -p=blastp+ synteny (PoFF) test: " [2/12] -p=blastp+ synteny (PoFF) test: if [ "/usr/bin/blastp" = "" ]; then\ echo "blastp missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_synteny -synteny -singles -p=blastp+ test/*.faa; \ set -e ; ./src/chk_test.pl test_synteny.proteinortho.tsv; \ set -e ; ./src/chk_test.pl test_synteny.poff.tsv; \ echo "passed"; \ fi 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 echo -n " [3/12] -p=diamond test: " [3/12] -p=diamond test: if [ "/usr/bin/diamond-aligner" = "" ]; then\ echo "diamond missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_diamond -p=diamond test/*.faa; \ set -e ; ./src/chk_test.pl test_diamond.proteinortho.tsv; \ echo "passed"; \ fi passed echo -n " [4/12] -p=diamond (--moresensitive) test (subparaBlast): " [4/12] -p=diamond (--moresensitive) test (subparaBlast): if [ "/usr/bin/diamond-aligner" = "" ]; then\ echo "diamond missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_diamondmoresensitive -p=diamond -subparaBlast="--more-sensitive" test/*.faa; \ set -e ; ./src/chk_test.pl test_diamondmoresensitive.proteinortho.tsv; \ echo "passed"; \ fi passed echo -n " [5/12] -p=lastp (lastal) test: " [5/12] -p=lastp (lastal) test: if [ "" = "" ]; then\ echo "lastal missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_lastp -p=lastp test/*.faa; \ set -e ; ./src/chk_test.pl test_lastp.proteinortho.tsv ; \ echo "passed"; \ fi lastal missing, skipping... echo -n " [6/12] -p=topaz test: " [6/12] -p=topaz test: if [ "" = "" ]; then\ echo "topaz missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_topaz -p=topaz test/*.faa; \ set -e ; ./src/chk_test.pl test_topaz.proteinortho.tsv; \ echo "passed"; \ fi topaz missing, skipping... echo -n " [7/12] -p=usearch test: " [7/12] -p=usearch test: if [ "" = "" ]; then\ echo "usearch missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_usearch -p=usearch test/*.faa; \ set -e ; ./src/chk_test.pl test_usearch.proteinortho.tsv; \ echo "passed"; \ fi usearch missing, skipping... echo -n " [8/12] -p=ublast test: " [8/12] -p=ublast test: if [ "" = "" ]; then\ echo "usearch missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_ublast -p=ublast test/*.faa; \ set -e ; ./src/chk_test.pl test_ublast.proteinortho.tsv; \ echo "passed"; \ fi usearch missing, skipping... echo -n " [9/12] -p=rapsearch test: " [9/12] -p=rapsearch test: if [ "" = "" ]; then\ echo "rapsearch missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_rapsearch -p=rapsearch test/*.faa; \ set -e ; ./src/chk_test.pl test_rapsearch.proteinortho.tsv; \ echo "passed"; \ fi rapsearch missing, skipping... echo -n " [10/12] -p=blatp (blat) test: " [10/12] -p=blatp (blat) test: if [ "" = "" ]; then\ echo "blat missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_blatp -p=blatp test/*.faa; \ set -e ; ./src/chk_test.pl test_blatp.proteinortho.tsv; \ echo "passed"; \ fi blat missing, skipping... echo -n " [11/12] -p=mmseqsp (mmseqs) test: " [11/12] -p=mmseqsp (mmseqs) test: if [ "" = "" ]; then\ echo "mmseqs missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_mmseqsp -p=mmseqsp test/*.faa; \ set -e ; ./src/chk_test.pl test_blatp.proteinortho.tsv; \ echo "passed"; \ fi mmseqs missing, skipping... echo -n " [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: " [12/12] -p=autoblast (automatically detect blastp,blastn,...) test: if [ "/usr/bin/blastp" = "" ]; then\ echo "ncbi-blast missing, skipping..."; \ else \ ./proteinortho6.pl -silent -force -project=test_autoblast -p=autoblast test/*.faa; \ set -e ; ./src/chk_test.pl test_autoblast.proteinortho.tsv; \ echo "passed"; \ fi passed Makefile:475: update target 'test_clean' due to: target is .PHONY echo "[TEST] Clean up all test files..."; \ rm -rf remove.graph* proteinortho_cache_test_* test.* test_* test/C.faa.* test/E.faa.* test/C2.faa.* test/L.faa.* test/M.faa.*> /dev/null 2>&1; [TEST] Clean up all test files... Makefile:283: update target 'test' due to: target is .PHONY echo "[TEST] All tests passed" [TEST] All tests passed make[2]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' rm test_* remove.* test/C_clean.faa rm: cannot remove 'test_*': No such file or directory rm: cannot remove 'remove.*': No such file or directory make[1]: *** [debian/rules:15: override_dh_auto_test] Error 1 shuffle=reverse make[1]: Leaving directory '/build/reproducible-path/proteinortho-6.3.1+dfsg' make: *** [debian/rules:10: binary] Error 2 shuffle=reverse dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2025-05-01T13:20:15Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup Thu, 01 May 2025 13:20:15 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died with exit 2) +------------------------------------------------------------------------------+ | Summary Thu, 01 May 2025 13:20:16 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 9692 Build-Time: 91 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 17 Job: proteinortho_6.3.1+dfsg-1 Machine Architecture: amd64 Package: proteinortho Package-Time: 120 Source-Version: 6.3.1+dfsg-1 Space: 9692 Status: attempted Version: 6.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2025-05-01T13:20:15Z Build needed 00:02:00, 9692k disk space E: Build failure (dpkg-buildpackage died with exit 2) DC-Status: Failed 121.200636585s