sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | barrnap 0.9+dfsg-4 (amd64) Mon, 30 Jun 2025 04:13:33 +0000 | +==============================================================================+ Package: barrnap Version: 0.9+dfsg-4 Source Version: 0.9+dfsg-4 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 30 Jun 2025 04:13:33 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup barrnap_0.9+dfsg-4 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup barrnap_0.9+dfsg-4 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 30 Jun 2025 04:13:34 +0000 | +------------------------------------------------------------------------------+ 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] Get:3 http://localhost:3142/debian sid InRelease [208 kB] Get:4 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid/main Sources T-2025-06-30-0204.28-F-2025-06-30-0204.28.pdiff [2990 B] Get:5 http://localhost:3142/debian sid/main Sources T-2025-06-30-0204.28-F-2025-06-30-0204.28.pdiff [2990 B] Fetched 275 kB in 5s (50.5 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 Mon, 30 Jun 2025 04:13:41 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/barrnap_0.9+dfsg-4.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 30 Jun 2025 04:13:41 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), hmmer, lua5.1, bedtools, build-essential Filtered Build-Depends: debhelper-compat (= 13), hmmer, lua5.1, bedtools, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ InRelease Get:2 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ Release [609 B] Ign:3 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ Release.gpg Get:4 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ Sources [625 B] Get:5 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ Packages [664 B] Fetched 1898 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 bedtools bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hmmer intltool-debian libarchive-zip-perl libdebhelper-perl libdivsufsort3 libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 lua5.1 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff hmmer-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bedtools bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base hmmer intltool-debian libarchive-zip-perl libdebhelper-perl libdivsufsort3 libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 lua5.1 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 12.6 MB of archives. After this operation, 49.8 MB of additional disk space will be used. Get:1 copy:/build/barrnap-nx1eVO/resolver-HNMCXB/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [872 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 lua5.1 amd64 5.1.5-11 [103 kB] Preconfiguring packages ... Fetched 12.6 MB in 0s (99.3 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23092 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... 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Selecting previously unselected package lua5.1. Preparing to unpack .../31-lua5.1_5.1.5-11_amd64.deb ... Unpacking lua5.1 (5.1.5-11) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../32-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up lua5.1 (5.1.5-11) ... update-alternatives: using /usr/bin/lua5.1 to provide /usr/bin/lua (lua-interpreter) in auto mode update-alternatives: using /usr/bin/luac5.1 to provide /usr/bin/luac (lua-compiler) in auto mode Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libdivsufsort3:amd64 (2.0.1-6+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up bedtools (2.31.1+dfsg-2) ... 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 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 dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up hmmer (3.4+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 30 Jun 2025 04:13:47 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Mon, 30 Jun 2025 04:13:47 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 bedtools_2.31.1+dfsg-2 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hmmer_3.4+dfsg-2 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdivsufsort3_2.0.1-6+b1 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.10+dfsg-1+b1 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 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnpth0t64_1.8-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 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_2.41-5 libsqlite3-0_3.46.1-6 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 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_257.7-1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 lua5.1_5.1.5-11 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 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_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 30 Jun 2025 04:13:47 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: barrnap Binary: barrnap Architecture: all Version: 0.9+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/barrnap Vcs-Git: https://salsa.debian.org/med-team/barrnap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), hmmer, lua5.1, bedtools Package-List: barrnap deb science optional arch=all Checksums-Sha1: c90352d95316d96f016540d1540ec198ecf3beb2 5783936 barrnap_0.9+dfsg.orig.tar.xz f81f6b438cf54cc5dbf4a2e1a69e6ddb0b311e01 702800 barrnap_0.9+dfsg-4.debian.tar.xz Checksums-Sha256: b780182b0154cf44915279bb57c1207b9b0aeb24e779fcd6de1a2b6779e89cc8 5783936 barrnap_0.9+dfsg.orig.tar.xz a6d6b925c2a6667433cc70b76e59e257b7d2792bbff541b68f03c57ae1f715d4 702800 barrnap_0.9+dfsg-4.debian.tar.xz Files: 944eaecec9c2fe9bdf344f6f33071ea6 5783936 barrnap_0.9+dfsg.orig.tar.xz d2ba201aafebc15283958e23556cb1b8 702800 barrnap_0.9+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmUFyCcACgkQPCZ2P2xn 5uJhmhAAjWrsPjrGxxym404LHnL0+iVEXONqACrAt7NuhhmUsXo94ljMx38pLQ8V OBjQ5VoKM14jJOs30Cb2+lBDsz9GzLATNJwJFbbi9ZbYSj21vw7dgsWsR9TxhNYn pfw4ggRFRHFnWa1GmG9+1ULdV3pnQqGZsEd8BEwXvvCtDtQILvP/6xRkFP6r9Mus 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Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 30 Jun 2025 04:13:48 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network barrnap_0.9+dfsg-4 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network barrnap_0.9+dfsg-4 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/barrnap-nx1eVO/barrnap-0.9+dfsg SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-f3706de3-8890-4f58-82c9-0de4c52ac0e3 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package barrnap dpkg-buildpackage: info: source version 0.9+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' rm -f *~ core foo DEADJOE make[1]: Leaving directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building barrnap using existing ./barrnap_0.9+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building barrnap in barrnap_0.9+dfsg-4.debian.tar.xz dpkg-source: info: building barrnap in barrnap_0.9+dfsg-4.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' # pass make[1]: Leaving directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' dh_auto_test make -j2 test make[1]: Entering directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' ./bin/barrnap examples/small.fna [barrnap] This is barrnap 0.9 [barrnap] Written by Torsten Seemann [barrnap] Obtained from https://github.com/tseemann/barrnap [barrnap] Detected operating system: linux [barrnap] Adding /build/barrnap-nx1eVO/barrnap-0.9+dfsg/bin/../binaries/linux to end of PATH [barrnap] Checking for dependencies: [barrnap] Found nhmmer - /usr/bin/nhmmer [barrnap] Found bedtools - /usr/bin/bedtools [barrnap] Will use 1 threads [barrnap] Setting evalue cutoff to 1e-06 [barrnap] Will tag genes < 0.8 of expected length. [barrnap] Will reject genes < 0.25 of expected length. [barrnap] Using database: /build/barrnap-nx1eVO/barrnap-0.9+dfsg/bin/../db/bac.hmm [barrnap] Scanning examples/small.fna for bac rRNA genes... please wait [barrnap] Command: nhmmer --cpu 1 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/build/barrnap-nx1eVO/barrnap-0.9+dfsg/bin/../db/bac.hmm' 'examples/small.fna' [barrnap] Found: 16S_rRNA P.marinus L=1480/1585 353314..354793 + 16S ribosomal RNA [barrnap] Found: 23S_rRNA P.marinus L=2871/3232 355464..358334 + 23S ribosomal RNA [barrnap] Found: 5S_rRNA P.marinus L=113/119 358433..358545 + 5S ribosomal RNA [barrnap] Found 3 ribosomal RNA features. [barrnap] Sorting features and outputting GFF3... [barrnap] Done. ##gff-version 3 P.marinus barrnap:0.9 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA P.marinus barrnap:0.9 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA P.marinus barrnap:0.9 rRNA 358433 358545 1.4e-12 + . Name=5S_rRNA;product=5S ribosomal RNA make[1]: Leaving directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' # pass make[1]: Leaving directory '/build/barrnap-nx1eVO/barrnap-0.9+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package barrnap: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'barrnap' in '../barrnap_0.9+dfsg-4_all.deb'. dpkg-genbuildinfo -O../barrnap_0.9+dfsg-4_amd64.buildinfo dpkg-genchanges -O../barrnap_0.9+dfsg-4_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-06-30T04:14:02Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 30 Jun 2025 04:14:02 +0000 | +------------------------------------------------------------------------------+ barrnap_0.9+dfsg-4_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 16 Sep 2023 16:36:40 +0200 Source: barrnap Binary: barrnap Architecture: source all Version: 0.9+dfsg-4 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: barrnap - rapid ribosomal RNA prediction Changes: barrnap (0.9+dfsg-4) unstable; urgency=medium . * Team upload. * d/patches/use_both_hmmsets: not needed since before 0.7+dfsg-1 * d/tests/control: hmmer is now available on arm64/armhf; test there as well. * d/patches/update_dbs: refresh the databases using the latest SILVA database which is DFSG compliant (CC-BY-4.0). * d/copyright: document the provenance and licensing for d/patches/update_dbs; update homepage URL * d/patches/use_debian_dirs: document author, no need to forward upstream Checksums-Sha1: aa3328321aaca6196150892303ecd1d33dfaa60f 1119 barrnap_0.9+dfsg-4.dsc f81f6b438cf54cc5dbf4a2e1a69e6ddb0b311e01 702800 barrnap_0.9+dfsg-4.debian.tar.xz c447d819ce3e3e7c18df7c9ec9c1cae3d57a91bb 525908 barrnap_0.9+dfsg-4_all.deb 31c24915da2d5f97a174aad6a7a3e34fe8d44480 5153 barrnap_0.9+dfsg-4_amd64.buildinfo Checksums-Sha256: 53abb7f362c560d4d121617b58c9053d0700fa0ae2eb2e2d74aba1ad35fd6fdf 1119 barrnap_0.9+dfsg-4.dsc a6d6b925c2a6667433cc70b76e59e257b7d2792bbff541b68f03c57ae1f715d4 702800 barrnap_0.9+dfsg-4.debian.tar.xz 6f1c68a498e4a407e0eb99b619760299741120b3856a6b60d6c307ac92564034 525908 barrnap_0.9+dfsg-4_all.deb 7deb990253078a4797af1ddafb415c1a29330d79bedae49e1559e4c4c77be321 5153 barrnap_0.9+dfsg-4_amd64.buildinfo Files: 962cf485a80c41d594d55c599093e8b8 1119 science optional barrnap_0.9+dfsg-4.dsc d2ba201aafebc15283958e23556cb1b8 702800 science optional barrnap_0.9+dfsg-4.debian.tar.xz 5c40cf562d19381e96be68d0bcdddeaf 525908 science optional barrnap_0.9+dfsg-4_all.deb 979025ad354e9c9cd9ea98024b2281bd 5153 science optional barrnap_0.9+dfsg-4_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Mon, 30 Jun 2025 04:14:03 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: barrnap Binary: barrnap Architecture: all source Version: 0.9+dfsg-4 Checksums-Md5: 962cf485a80c41d594d55c599093e8b8 1119 barrnap_0.9+dfsg-4.dsc 5c40cf562d19381e96be68d0bcdddeaf 525908 barrnap_0.9+dfsg-4_all.deb Checksums-Sha1: aa3328321aaca6196150892303ecd1d33dfaa60f 1119 barrnap_0.9+dfsg-4.dsc c447d819ce3e3e7c18df7c9ec9c1cae3d57a91bb 525908 barrnap_0.9+dfsg-4_all.deb Checksums-Sha256: 53abb7f362c560d4d121617b58c9053d0700fa0ae2eb2e2d74aba1ad35fd6fdf 1119 barrnap_0.9+dfsg-4.dsc 6f1c68a498e4a407e0eb99b619760299741120b3856a6b60d6c307ac92564034 525908 barrnap_0.9+dfsg-4_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 30 Jun 2025 04:14:02 +0000 Build-Path: /build/barrnap-nx1eVO/barrnap-0.9+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), bedtools (= 2.31.1+dfsg-2), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hmmer (= 3.4+dfsg-2), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdivsufsort3 (= 2.0.1-6+b1), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libhwasan0 (= 14.2.0-19), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41-5), liblsan0 (= 14.2.0-19), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libquadmath0 (= 14.2.0-19), libreadline8t64 (= 8.2-6), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), lua5.1 (= 5.1.5-11), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), po-debconf (= 1.0.21+nmu1), readline-common (= 8.2-6), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1694875000" +------------------------------------------------------------------------------+ | Package contents Mon, 30 Jun 2025 04:14:03 +0000 | +------------------------------------------------------------------------------+ barrnap_0.9+dfsg-4_all.deb -------------------------- new Debian package, version 2.0. size 525908 bytes: control archive=1052 bytes. 813 bytes, 18 lines control 580 bytes, 9 lines md5sums Package: barrnap Version: 0.9+dfsg-4 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 3170 Depends: perl:any, hmmer, bedtools Section: science Priority: optional Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml Description: rapid ribosomal RNA prediction Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). . It takes FASTA DNA sequence as input, and writes GFF3 as output. It uses the NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. drwxr-xr-x root/root 0 2023-09-16 14:36 ./ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/bin/ -rwxr-xr-x root/root 9286 2023-09-16 14:36 ./usr/bin/barrnap drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/barrnap/ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/barrnap/db/ -rw-r--r-- root/root 840176 2023-09-16 14:36 ./usr/share/barrnap/db/arc.hmm -rw-r--r-- root/root 806590 2023-09-16 14:36 ./usr/share/barrnap/db/bac.hmm -rw-r--r-- root/root 1035235 2023-09-16 14:36 ./usr/share/barrnap/db/euk.hmm -rw-r--r-- root/root 530066 2023-09-16 14:36 ./usr/share/barrnap/db/mito.hmm drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/doc/barrnap/ -rw-r--r-- root/root 2819 2023-09-16 14:36 ./usr/share/doc/barrnap/README.md.gz -rw-r--r-- root/root 1033 2023-09-16 14:36 ./usr/share/doc/barrnap/changelog.Debian.gz -rw-r--r-- root/root 4194 2023-09-16 14:36 ./usr/share/doc/barrnap/copyright drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/man/ drwxr-xr-x root/root 0 2023-09-16 14:36 ./usr/share/man/man1/ -rw-r--r-- root/root 619 2023-09-16 14:36 ./usr/share/man/man1/barrnap.1.gz +------------------------------------------------------------------------------+ | Post Build Mon, 30 Jun 2025 04:14:03 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 30 Jun 2025 04:14:03 +0000 | +------------------------------------------------------------------------------+ Purging /build/barrnap-nx1eVO Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 30 Jun 2025 04:14:05 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 34308 Build-Time: 14 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/barrnap_0.9+dfsg-4.dsc Machine Architecture: amd64 Package: barrnap Package-Time: 29 Source-Version: 0.9+dfsg-4 Space: 34308 Status: successful Version: 0.9+dfsg-4 -------------------------------------------------------------------------------- Finished at 2025-06-30T04:14:02Z Build needed 00:00:29, 34308k disk space