sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | sspace 2.1.1+dfsg-7 (amd64) Mon, 05 Aug 2024 02:09:40 +0000 | +==============================================================================+ Package: sspace Version: 2.1.1+dfsg-7 Source Version: 2.1.1+dfsg-7 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-00c038f0-72de-4ae9-897f-dfe70abf0967' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup sspace_2.1.1+dfsg-7 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup sspace_2.1.1+dfsg-7 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/sspace-JuLutl/resolver-MLZBOw' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/sspace_2.1.1+dfsg-7.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/sspace-JuLutl/sspace-2.1.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/sspace-JuLutl' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), recode, python3, asciidoctor, bowtie, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), recode, python3, asciidoctor, bowtie, 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 [655 B] Get:5 copy:/<>/apt_archive ./ Packages [687 B] Fetched 1951 B in 0s (108 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bowtie bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libedit2 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libncurses6 libpipeline1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librecode3 libruby libruby3.1t64 libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types netbase openssl po-debconf python3 python3-minimal python3.12 python3.12-minimal rake recode ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration sensible-utils tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc bowtie-examples dh-make gettext-doc libasprintf-dev libgettextpo-dev groff 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 ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bowtie bsdextrautils ca-certificates debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libedit2 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libncurses6 libpipeline1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librecode3 libruby libruby3.1t64 libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types netbase openssl po-debconf python3 python3-minimal python3.12 python3.12-minimal rake recode ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration sbuild-build-depends-main-dummy sensible-utils tzdata 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 36.4 MB of archives. After this operation, 143 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.4-3 [812 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.4-3 [2137 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.4-1 [26.5 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.4-3 [1950 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.4-3 [664 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.4-1 [9500 B] Get:12 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.4-1 [27.6 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.1-2 [1380 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-1 [96.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get:26 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b4 [15.4 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.3 [5399 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.3 [664 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get:37 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get:39 http://deb.debian.org/debian unstable/main amd64 ruby-asciidoctor all 2.0.23-1 [214 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 asciidoctor all 2.0.23-1 [88.7 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 bowtie amd64 1.3.1-3 [1627 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:53 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 librecode3 amd64 3.7.14-1 [232 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 recode amd64 3.7.14-1 [169 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.4 MB in 0s (97.3 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 22966 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.4-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.4-3_amd64.deb ... Unpacking python3.12-minimal (3.12.4-3) ... Setting up libpython3.12-minimal:amd64 (3.12.4-3) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 23286 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.4-1_amd64.deb ... Unpacking python3-minimal (3.12.4-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../4-libpython3.12-stdlib_3.12.4-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../5-python3.12_3.12.4-3_amd64.deb ... Unpacking python3.12 (3.12.4-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.12.4-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.4-1) ... Setting up python3-minimal (3.12.4-1) ... Selecting previously unselected package python3. (Reading database ... 24256 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.4-1_amd64.deb ... Unpacking python3 (3.12.4-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.3.1-2_amd64.deb ... Unpacking openssl (3.3.1-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-1_amd64.deb ... Unpacking bsdextrautils (2.40.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.1-2_amd64.deb ... Unpacking man-db (2.12.1-2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../13-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../14-rake_13.2.1-1_all.deb ... Unpacking rake (13.2.1-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../16-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.3-2_all.deb ... Unpacking ruby-xmlrpc (0.3.3-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../18-ruby-sdbm_1.0.0-5+b4_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b4) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../19-libedit2_3.1-20240517-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240517-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../20-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../21-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package libruby3.1t64:amd64. Preparing to unpack .../22-libruby3.1t64_3.1.2-8.3_amd64.deb ... Unpacking libruby3.1t64:amd64 (3.1.2-8.3) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../23-ruby3.1_3.1.2-8.3_amd64.deb ... Unpacking ruby3.1 (3.1.2-8.3) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../24-libruby_1%3a3.1+nmu1_amd64.deb ... Unpacking libruby:amd64 (1:3.1+nmu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../25-ruby-rubygems_3.4.20-1_all.deb ... Unpacking ruby-rubygems (3.4.20-1) ... Selecting previously unselected package ruby. Preparing to unpack .../26-ruby_1%3a3.1+nmu1_amd64.deb ... Unpacking ruby (1:3.1+nmu1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../27-ruby-asciidoctor_2.0.23-1_all.deb ... Unpacking ruby-asciidoctor (2.0.23-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../28-asciidoctor_2.0.23-1_all.deb ... Unpacking asciidoctor (2.0.23-1) ... Selecting previously unselected package m4. Preparing to unpack .../29-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../30-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../31-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../32-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../33-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package bowtie. Preparing to unpack .../34-bowtie_1.3.1-3_amd64.deb ... Unpacking bowtie (1.3.1-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../35-libdebhelper-perl_13.16_all.deb ... Unpacking libdebhelper-perl (13.16) ... Selecting previously unselected package libtool. Preparing to unpack .../36-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../37-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../38-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../39-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../40-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../41-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../42-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../43-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../44-libxml2_2.12.7+dfsg-3+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-3+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../45-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../46-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../47-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../48-debhelper_13.16_all.deb ... Unpacking debhelper (13.16) ... Selecting previously unselected package libfakeroot:amd64. Preparing to unpack .../49-libfakeroot_1.35.1-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.35.1-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../50-fakeroot_1.35.1-1_amd64.deb ... Unpacking fakeroot (1.35.1-1) ... Selecting previously unselected package librecode3:amd64. Preparing to unpack .../51-librecode3_3.7.14-1_amd64.deb ... Unpacking librecode3:amd64 (3.7.14-1) ... Selecting previously unselected package recode. Preparing to unpack .../52-recode_3.7.14-1_amd64.deb ... Unpacking recode (3.7.14-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../53-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up librecode3:amd64 (3.7.14-1) ... Setting up libdebhelper-perl (13.16) ... Setting up libedit2:amd64 (3.1-20240517-1) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... 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: Mon Aug 5 02:10:02 UTC 2024. Universal Time is now: Mon Aug 5 02:10:02 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 recode (3.7.14-1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up dwz (0.15-1+b1) ... 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 sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up openssl (3.3.1-2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... 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 gettext (0.22.5-2) ... 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 ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up dh-strip-nondeterminism (1.14.0-1) ... 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 rubygems-integration (1.18) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up bowtie (1.3.1-3) ... Setting up debhelper (13.16) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b4) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up libruby3.1t64:amd64 (3.1.2-8.3) ... Setting up ruby3.1 (3.1.2-8.3) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up ruby-asciidoctor (2.0.23-1) ... Setting up asciidoctor (2.0.23-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | 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 asciidoctor_2.0.23-1 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 bowtie_1.3.1-3 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 ca-certificates_20240203 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 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 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 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 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 libblkid1_2.40.2-1 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_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 libeatmydata1_131-2 libedit2_3.1-20240517-1 libelf1t64_0.191-2 libexpat1_2.6.2-1 libfakeroot_1.35.1-1 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 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libhogweed6t64_3.10-1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 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 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-1 libpipeline1_1.5.7-2 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 librecode3_3.7.14-1 libruby_1:3.1+nmu1 libruby3.1t64_3.1.2-8.3 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssl3t64_3.3.1-2 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 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 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 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 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl_3.3.1-2 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 python3_3.12.4-1 python3-minimal_3.12.4-1 python3.12_3.12.4-3 python3.12-minimal_3.12.4-3 rake_13.2.1-1 readline-common_8.2-4 recode_3.7.14-1 rpcsvc-proto_1.4.3-1 ruby_1:3.1+nmu1 ruby-asciidoctor_2.0.23-1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5+b4 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.3-2 ruby3.1_3.1.2-8.3 rubygems-integration_1.18 sbuild-build-depends-main-dummy_0.invalid.0 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 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: sspace Binary: sspace Architecture: all Version: 2.1.1+dfsg-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss Homepage: https://github.com/nsoranzo/sspace_basic Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/sspace Vcs-Git: https://salsa.debian.org/med-team/sspace.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), recode, python3, asciidoctor, bowtie Package-List: sspace deb science optional arch=all Checksums-Sha1: 0911ac377d0cdfa0611cd27df211a850cddf648a 1234924 sspace_2.1.1+dfsg.orig.tar.xz 133e45da64647d8d13e45d8445fc0a942e5e4876 501040 sspace_2.1.1+dfsg-7.debian.tar.xz Checksums-Sha256: 5bbb1cfd1e68af66fd31ab3d9720c450a9acf9a2a4bf9bde7e8e54a859b04aa1 1234924 sspace_2.1.1+dfsg.orig.tar.xz 8eb1eab0c3e3293c0817c9aa34fc038ac5daa60ec0452a79b219a55e2a42c8ab 501040 sspace_2.1.1+dfsg-7.debian.tar.xz Files: 2dc72080013bc674ff8a1fb5190381f2 1234924 sspace_2.1.1+dfsg.orig.tar.xz 08838d5d2dfaf699793a4007a7955722 501040 sspace_2.1.1+dfsg-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmNWkQsACgkQ6NN64vCf SHLuwA//VZYFlKxAh4pVodWLzPGtK0GCAlZ3T9Yj5IFSLId3uzcO+5u8nryUu0bF j+PqOczQFWZgLW8ZuH4vs7IIAb+vJNeSle0EdU9CrHFp2fdRQhB2KH2ePGAeA3xn eUs6DE5KwuEHYTqXQptqMX3dWDqxCe3joNsdLEDVYkACuCK9vv5H50lGk486D7rj iPUVzy/wq9wmL9Hw3V8ewV2S+s/kl/SX6eTZtaFGJCWtJgQW9BZGXkj27PI74+Pb DLh/OaynDI59Pm4nvLGwSYyyGPivljb+rHmYfLPkGcYEA38+CI4QmYp5jgLRTp67 +peTpUrGmMsEEQCiVgCT0oK1ARcq2qpMtIkudzQezlUTHWLWjBPIb+qZvdd3gfIi P+VWJREoNBtIoIOzb/8hnAP3g5B+IRQYnY+oZFFKhl6GfYbu7RuQWU/EP108pfb0 s8Djo1vNJ2YHhpi3WYGBQAWef7mDWhcKNwjzAK6N2bQqL4Cl4lKY+PAnP+/8tCg7 LHy1Hq4x+He+4vw4yQH/Af4s1IfnwQlgFrK/9BUXEk7ylvA0eEbvL2K19l/a0vmw JqXFjVh+8c64ZP6bsZQSfwC/kjcCvk2L4JFNhTYfI/rRwzuDj3xiq/emtl+7g8hc iF6DBMIQRd2wpgW26ESmC0bh5HgqmHf6W/0nzWOVRtKFSbeR0EU= =8htq -----END PGP SIGNATURE----- gpgv: Signature made Mon Oct 24 13:20:11 2022 UTC gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sspace_2.1.1+dfsg-7.dsc: no acceptable signature found dpkg-source: info: extracting sspace in /<> dpkg-source: info: unpacking sspace_2.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking sspace_2.1.1+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying shebangs.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network sspace_2.1.1+dfsg-7 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network sspace_2.1.1+dfsg-7 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-00c038f0-72de-4ae9-897f-dfe70abf0967 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 sspace dpkg-buildpackage: info: source version 2.1.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -f debian/sspace.1 make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building sspace using existing ./sspace_2.1.1+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building sspace in sspace_2.1.1+dfsg-7.debian.tar.xz dpkg-source: info: building sspace in sspace_2.1.1+dfsg-7.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_test make[1]: Entering directory '/<>' debian/tests/example-tests /<>/SSPACE_Basic.pl Your inserted inputs on [SSPACE_Basic v2.1] at Mon Aug 5 02:10:15 2024: Required inputs: -l = libraries.txt -s = contigs_abyss.fasta -b = standard_output Optional inputs: -x = 0 -z = 0 -k = 5 -a = 0.7 -n = 15 -T = 1 -p = 0 =>Mon Aug 5 02:10:15 2024: Reading, filtering and converting input sequences of library file initiated Reading read-pairs lib1.1 @ 0 ------------------------------------------------------------ =>Mon Aug 5 02:10:15 2024: Storing contigs to format for scaffolding 100 200 300 400 500 LIBRARY lib1 ------------------------------------------------------------ =>Mon Aug 5 02:10:15 2024: Reading contig file =>Mon Aug 5 02:10:15 2024: Building Bowtie index for contigs =>Mon Aug 5 02:10:15 2024: Mapping reads to contigs. Reading bowtie output and pairing contigs Setting the index via positional argument will be deprecated in a future release. Please use -x option instead. # reads processed: 19924 # reads with at least one alignment: 1879 (9.43%) # reads that failed to align: 18045 (90.57%) Reported 1879 alignments =>Mon Aug 5 02:10:15 2024: Building scaffolds file 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 =>Mon Aug 5 02:10:15 2024: Merging contigs and creating FASTA file of scaffolds 100 200 300 400 500 ------------------------------------------------------------ =>Mon Aug 5 02:10:15 2024: Creating summary file ************************************************** Process run succesfully on Mon Aug 5 02:10:15 2024 in 0 minutes and 0 seconds make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/sspace/ debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install find debian -name "*.pl" -exec recode ibmpc.. \{\} \; recode: /<>/debian/sspace/usr/share/sspace/SSPACE_Basic.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/SSPACE_Basic.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/tools/sam_bam2tab.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/tools/fq_all2std.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/tools/qseq2fastq.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/tools/qseq2fasta.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/tools/estimate_insert_size.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/bin/PairingAndScaffolding.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/bin/readLibFiles.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' recode: /<>/debian/sspace/usr/share/sspace/bin/ExtendOrFormatContigs.pl failed: Ambiguous output in step `ISO-10646-UCS-4..UTF-8' chmod -x debian/sspace/usr/share/sspace/tools/TRIMMING_PAIRED_READS.README \ debian/sspace/usr/share/sspace/tools/TQS.readme \ debian/sspace/usr/share/sspace/dotlib/DotLib.pm 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 debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples chmod -x debian/sspace/usr/share/doc/sspace/examples/libraries.txt make[1]: Leaving directory '/<>' debian/rules override_dh_installman make[1]: Entering directory '/<>' asciidoctor -a docdate='' -b manpage debian/sspace.1.adoc dh_installman make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name contigs_abyss.fasta -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'sspace' in '../sspace_2.1.1+dfsg-7_all.deb'. dpkg-genbuildinfo -O../sspace_2.1.1+dfsg-7_amd64.buildinfo dpkg-genchanges -O../sspace_2.1.1+dfsg-7_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 2024-08-05T02:10:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ sspace_2.1.1+dfsg-7_amd64.changes: ---------------------------------- Format: 1.8 Date: Mon, 24 Oct 2022 15:08:39 +0200 Source: sspace Binary: sspace Architecture: source all Version: 2.1.1+dfsg-7 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: sspace - scaffolding pre-assembled contigs after extension Changes: sspace (2.1.1+dfsg-7) unstable; urgency=medium . * Bump Standards-Version. * Update email and dates in d/copyright. * Fix watchfile. Checksums-Sha1: 6661f4bd7aef8a58b760c4dd8eb99ba3281971e4 1154 sspace_2.1.1+dfsg-7.dsc aaf82396956f89d52d371fb3f960dd055a1738d0 501048 sspace_2.1.1+dfsg-7.debian.tar.xz d7667bc2bbfe99b750084e40a3c1817c5eabb083 1237164 sspace_2.1.1+dfsg-7_all.deb 90e22ff26e026ecc2eccd8279960aa60257027a2 6064 sspace_2.1.1+dfsg-7_amd64.buildinfo Checksums-Sha256: 0269eb34fa3c760a7cda86f1dceecec0cb9997cc5b99e5152d008fea2b4220fc 1154 sspace_2.1.1+dfsg-7.dsc d0c79cdd61077f61c47b293d4a024a05a3918a76b1d689dbb5b380533c831130 501048 sspace_2.1.1+dfsg-7.debian.tar.xz eb0775388a56dff7c40751d06e23b65aa09f08a223855c1bd09abb0f08ae32b7 1237164 sspace_2.1.1+dfsg-7_all.deb dd5a9b61886c37379cd9ad65a681bfefc29cfa283d549d134095b1e9ea466c9a 6064 sspace_2.1.1+dfsg-7_amd64.buildinfo Files: 7acfe8bd70c49d5f6d2f3589af22358a 1154 science optional sspace_2.1.1+dfsg-7.dsc ddde861938fffd341c0f8f1a7da30d5c 501048 science optional sspace_2.1.1+dfsg-7.debian.tar.xz 2adda92bb733c92d03e35578590b442f 1237164 science optional sspace_2.1.1+dfsg-7_all.deb 37f0478777c3951c4be7ce3d3f63ac27 6064 science optional sspace_2.1.1+dfsg-7_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: sspace Binary: sspace Architecture: all source Version: 2.1.1+dfsg-7 Checksums-Md5: 7acfe8bd70c49d5f6d2f3589af22358a 1154 sspace_2.1.1+dfsg-7.dsc 2adda92bb733c92d03e35578590b442f 1237164 sspace_2.1.1+dfsg-7_all.deb Checksums-Sha1: 6661f4bd7aef8a58b760c4dd8eb99ba3281971e4 1154 sspace_2.1.1+dfsg-7.dsc d7667bc2bbfe99b750084e40a3c1817c5eabb083 1237164 sspace_2.1.1+dfsg-7_all.deb Checksums-Sha256: 0269eb34fa3c760a7cda86f1dceecec0cb9997cc5b99e5152d008fea2b4220fc 1154 sspace_2.1.1+dfsg-7.dsc eb0775388a56dff7c40751d06e23b65aa09f08a223855c1bd09abb0f08ae32b7 1237164 sspace_2.1.1+dfsg-7_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 05 Aug 2024 02:10:23 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.23-1), 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), bowtie (= 1.3.1-3), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), 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), 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), libblkid1 (= 2.40.2-1), libbsd0 (= 0.12.2-1), 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), libedit2 (= 3.1-20240517-1), 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), 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), liblsan0 (= 14.2.0-1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), 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), 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), librecode3 (= 3.7.14-1), libruby (= 1:3.1+nmu1), libruby3.1t64 (= 3.1.2-8.3), 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), libxml2 (= 2.12.7+dfsg-3+b1), libyaml-0-2 (= 0.2.5-1+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), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openssl (= 3.3.1-2), 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), python3 (= 3.12.4-1), python3-minimal (= 3.12.4-1), python3.12 (= 3.12.4-3), python3.12-minimal (= 3.12.4-3), rake (= 13.2.1-1), readline-common (= 8.2-4), recode (= 3.7.14-1), rpcsvc-proto (= 1.4.3-1), ruby (= 1:3.1+nmu1), ruby-asciidoctor (= 2.0.23-1), ruby-net-telnet (= 0.2.0-1), ruby-rubygems (= 3.4.20-1), ruby-sdbm (= 1.0.0-5+b4), ruby-webrick (= 1.8.1-1), ruby-xmlrpc (= 0.3.3-2), ruby3.1 (= 3.1.2-8.3), rubygems-integration (= 1.18), 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="1666616919" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ sspace_2.1.1+dfsg-7_all.deb --------------------------- new Debian package, version 2.0. size 1237164 bytes: control archive=1484 bytes. 842 bytes, 20 lines control 1639 bytes, 23 lines md5sums Package: sspace Version: 2.1.1+dfsg-7 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 4651 Depends: perl:any, python3:any, bowtie Section: science Priority: optional Homepage: https://github.com/nsoranzo/sspace_basic Description: scaffolding pre-assembled contigs after extension SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension (SSPACE) is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination. . SSPACE is built based on SSAKE. Code of SSAKE is changed to be able to extend and scaffold pre-assembled contigs for multiple paired reads libraries. . This is the free 'basic' version of SSPACE. The non-free 'standard' version is available directly from Baseclear. drwxr-xr-x root/root 0 2022-10-24 13:08 ./ drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/ drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/bin/ -rwxr-xr-x root/root 305 2019-12-20 13:17 ./usr/bin/sspace drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/ drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/doc/sspace/ -rw-r--r-- root/root 1263 2019-12-20 13:17 ./usr/share/doc/sspace/README.Debian -rw-r--r-- root/root 11605 2016-02-09 11:38 ./usr/share/doc/sspace/README.gz -rw-r--r-- root/root 732 2022-10-24 13:08 ./usr/share/doc/sspace/changelog.Debian.gz -rw-r--r-- root/root 1587 2022-10-24 13:08 ./usr/share/doc/sspace/copyright drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/doc/sspace/examples/ -rw-r--r-- root/root 4571848 2016-02-09 11:38 ./usr/share/doc/sspace/examples/contigs_abyss.fasta -rw-r--r-- root/root 52 2016-02-09 11:38 ./usr/share/doc/sspace/examples/libraries.txt drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/man/ drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/man/man1/ -rw-r--r-- root/root 1379 2022-10-24 13:08 ./usr/share/man/man1/sspace.1.gz drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/sspace/ -rwxr-xr-x root/root 31022 2016-02-09 11:38 ./usr/share/sspace/SSPACE_Basic.pl lrwxrwxrwx root/root 0 2022-10-24 13:08 ./usr/share/sspace/SSPACE_Basic_v2.0.pl -> SSPACE_Basic.pl drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/sspace/bin/ -rwxr-xr-x root/root 16674 2022-10-24 13:08 ./usr/share/sspace/bin/ExtendOrFormatContigs.pl -rwxr-xr-x root/root 40486 2022-10-24 13:08 ./usr/share/sspace/bin/PairingAndScaffolding.pl -rwxr-xr-x root/root 7702 2022-10-24 13:08 ./usr/share/sspace/bin/readLibFiles.pl drwxr-xr-x root/root 0 2016-02-09 11:38 ./usr/share/sspace/dotlib/ -rw-r--r-- root/root 4696 2016-02-09 11:38 ./usr/share/sspace/dotlib/DotLib.pm drwxr-xr-x root/root 0 2022-10-24 13:08 ./usr/share/sspace/tools/ -rwxr-xr-x root/root 8028 2022-10-24 13:08 ./usr/share/sspace/tools/TQS.py -rw-r--r-- root/root 2277 2022-10-24 13:08 ./usr/share/sspace/tools/TQS.readme -rwxr-xr-x root/root 5093 2022-10-24 13:08 ./usr/share/sspace/tools/TQSexport.py -rwxr-xr-x root/root 5512 2022-10-24 13:08 ./usr/share/sspace/tools/TQSfastq.py -rw-r--r-- root/root 3179 2016-02-09 11:38 ./usr/share/sspace/tools/TRIMMING_PAIRED_READS.README -rwxr-xr-x root/root 7340 2022-10-24 13:08 ./usr/share/sspace/tools/estimate_insert_size.pl -rwxr-xr-x root/root 7576 2022-10-24 13:08 ./usr/share/sspace/tools/fq_all2std.pl -rwxr-xr-x root/root 482 2016-02-09 11:38 ./usr/share/sspace/tools/qseq2fasta.pl -rwxr-xr-x root/root 382 2016-02-09 11:38 ./usr/share/sspace/tools/qseq2fastq.pl -rwxr-xr-x root/root 4608 2022-10-24 13:08 ./usr/share/sspace/tools/sam_bam2tab.pl +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 13364 Build-Time: 11 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 22 Job: /srv/debomatic/incoming/sspace_2.1.1+dfsg-7.dsc Machine Architecture: amd64 Package: sspace Package-Time: 43 Source-Version: 2.1.1+dfsg-7 Space: 13364 Status: successful Version: 2.1.1+dfsg-7 -------------------------------------------------------------------------------- Finished at 2024-08-05T02:10:23Z Build needed 00:00:43, 13364k disk space