sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | clonalorigin 1.0-8 (amd64) Sun, 17 Aug 2025 09:51:31 +0000 | +==============================================================================+ Package: clonalorigin Version: 1.0-8 Source Version: 1.0-8 Distribution: perl-5.42-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 Sun, 17 Aug 2025 09:51:32 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-8 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-8 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 17 Aug 2025 09:51:32 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 Packages [547 kB] Get:3 http://deb.debian.org/debian unstable InRelease [216 kB] Get:4 http://deb.debian.org/debian sid InRelease [216 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [71.2 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [71.2 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [56.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [56.4 kB] Fetched 686 kB in 8s (87.8 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (87.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14970 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.68) ... Setting up init-system-helpers (1.69) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Sun, 17 Aug 2025 09:51:44 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/clonalorigin_1.0-8.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 17 Aug 2025 09:51:45 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libgsl-dev, rename, build-essential Filtered Build-Depends: debhelper-compat (= 13), libgsl-dev, rename, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ InRelease Get:2 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ Release [609 B] Ign:3 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ Release.gpg Get:4 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ Sources [620 B] Get:5 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ Packages [659 B] Fetched 1888 B in 0s (128 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgsl-dev libgsl28 libgslcblas0 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf rename sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 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 bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgsl-dev libgsl28 libgslcblas0 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf rename sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 51.9 MB of additional disk space will be used. Get:1 copy:/build/clonalorigin-RikKKw/resolver-ceS8og/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [868 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+b1 [244 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 2.41.1-1 [94.7 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 libdebhelper-perl all 13.25 [91.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Preconfiguring packages ... Fetched 13.1 MB in 0s (77.7 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14972 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+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-1_amd64.deb ... Unpacking bsdextrautils (2.41.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.25_all.deb ... Unpacking libdebhelper-perl (13.25) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. 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Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../25-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 .../26-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../27-debhelper_13.25_all.deb ... Unpacking debhelper (13.25) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../28-libgslcblas0_2.8+dfsg-5_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../29-libgsl28_2.8+dfsg-5_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../30-libgsl-dev_2.8+dfsg-5_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package rename. Preparing to unpack .../31-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... 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 (2.41.1-1) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.1) ... Setting up libdebhelper-perl (13.25) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.46-5) ... 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 libgsl28:amd64 (2.8+dfsg-5) ... 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+b1) ... Setting up libgsl-dev (2.8+dfsg-5) ... 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 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 (13.25) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 17 Aug 2025 09:51:51 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 17 Aug 2025 09:51:52 +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_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 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++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libblkid1_2.41.1-1 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-1 libgpg-error0_1.55-2 libgprofng0_2.45-4 libgsl-dev_2.8+dfsg-5 libgsl28_2.8+dfsg-5 libgslcblas0_2.8+dfsg-5 libhogweed6t64_3.10.1-1 libhwasan0_15.2.0-1 libidn2-0_2.3.8-3 libisl23_0.27-1 libitm1_15.2.0-1 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-1 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_2.41.1-1 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 libperl5.40_5.40.1-6 libperl5.42_5.42.0-1 libpipeline1_1.5.8-1 libquadmath0_15.2.0-1 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 libsframe2_2.45-4 libsmartcols1_2.41.1-1 libsqlite3-0_3.46.1-7 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 libsystemd0_258~rc2-2 libtasn1-6_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libudev1_258~rc2-2 libunistring5_1.3-2 libuuid1_2.41.1-1 libxml2-16_2.14.5+dfsg-0.1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 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_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rename_2.02-1 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 util-linux_2.41.1-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sun, 17 Aug 2025 09:51:52 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: clonalorigin Binary: clonalorigin Architecture: any Version: 1.0-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/xavierdidelot/clonalorigin Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/clonalorigin Vcs-Git: https://salsa.debian.org/med-team/clonalorigin.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libgsl-dev, rename Package-List: clonalorigin deb science optional arch=any Checksums-Sha1: a7bc183ea6aea575a5f5fa9217d9112d2ff4884f 185865 clonalorigin_1.0.orig.tar.gz 8b84785b3d7ffb55e62b2b9932c4c62ec9900f03 10608 clonalorigin_1.0-8.debian.tar.xz Checksums-Sha256: 73962415160b8b496c81d3e9cbbf68f76c02caf4dd6b41860f01d493b71c6e3a 185865 clonalorigin_1.0.orig.tar.gz 192e0da0642eea3f9e86d40b535ac89c900be9cfe557d163ca29a54e7f479882 10608 clonalorigin_1.0-8.debian.tar.xz Files: 310a0c5714e7629c052ab4da50c90f44 185865 clonalorigin_1.0.orig.tar.gz 905b8b38da217ad00e12e9f849ec267d 10608 clonalorigin_1.0-8.debian.tar.xz Dgit: b3fc1b67fb518bb450b668e97a3abd1aad93e880 debian archive/debian/1.0-8 https://git.dgit.debian.org/clonalorigin -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmWOuYIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqpLRAAlNK1ErVhpNbWQg9JbH8pUmb/hafe 4sqdQYUZfy+tcsLF6Z/Cg4ZNUVTOXnZqkio9j+w9Jnkwso6uEwtsnrYuZpkgyq6b bo9Zw72KXMObXOkYNXFyOC8eDJ2GW0ja60v7uCWDeews4/uUEuHVvUa+WMHtpwP5 d5L4LzhMfOpt4ph7rwWewJygNSMfS3x7TIWa+iJbdKxppxgvWFDHbVv42405HpFu c7aYVdJIErhIpBEl19i+xt+REkCHbnxF/UPjWzThMd+H9+H7F8xEdqi9gSDbmRWY NYxxit/A9HWIds1sWCho4MsMCdDTWpaxUF/rskxLI6HmqreIuFFlE2J4WJYfnT4a qe3JH/FblMoQQdEFHifif0ST0kyb5h4HyoL2syQ7oDidEP2UmpQ+C6G0Tbnd3DA3 Hlq+cjYEUAZPTDNtoWJi0IBjOIu6rPCkUggW61KnlD/HvKwl9FOatdVOGuQj63Iv allzBEyfG/EC56TyDMZgZfKOMv0ri6Uzb8RAaQci8qEWPyg7VXXYMZNEciK1xrIC sxGgwziuEQVF8ZeiLgGNKom/u6GYBHZYiiaQp8KDIHCexcXz9VabN1sN9/7bxMVK n/5mk6Re+mqku5JhnOMekh/QxstEALo+Td53zjLbVItWBfMy39LYnUBhKnAVOnw3 TGWTkPv8gXLFCSg= =dgh7 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-8.dsc: no acceptable signature found dpkg-source: info: extracting clonalorigin in /build/clonalorigin-RikKKw/clonalorigin-1.0 dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz dpkg-source: info: unpacking clonalorigin_1.0-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying portability.patch dpkg-source: info: applying gcc-11.patch dpkg-source: info: applying shorten-test.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 17 Aug 2025 09:51:52 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-8 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-8 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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/clonalorigin-RikKKw/clonalorigin-1.0 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-d2164484-f37c-4a5d-b906-1d0936501fa7 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 clonalorigin dpkg-buildpackage: info: source version 1.0-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=warg dh_auto_clean -O--sourcedirectory=warg debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' test ! -e warg/src/truth.xml.preserve \ || mv -v warg/src/truth.xml.preserve warg/src/truth.xml make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' dh_autoreconf_clean -O--sourcedirectory=warg dh_clean -O--sourcedirectory=warg dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building clonalorigin using existing ./clonalorigin_1.0.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building clonalorigin in clonalorigin_1.0-8.debian.tar.xz dpkg-source: info: building clonalorigin in clonalorigin_1.0-8.dsc debian/rules binary dh binary --sourcedirectory=warg dh_update_autotools_config -O--sourcedirectory=warg dh_autoreconf -O--sourcedirectory=warg configure.ac:58: warning: The macro 'AC_TRY_RUN' is obsolete. configure.ac:58: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... m4/gsl.m4:5: AX_PATH_GSL is expanded from... configure.ac:58: the top level configure.ac:58: warning: The macro 'AC_TRY_LINK' is obsolete. configure.ac:58: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... m4/gsl.m4:5: AX_PATH_GSL is expanded from... configure.ac:58: the top level configure.ac:41: installing 'config/compile' configure.ac:9: installing 'config/install-sh' configure.ac:9: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' parallel-tests: installing 'config/test-driver' debian/rules execute_before_dh_auto_configure make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' cp -v warg/src/truth.xml warg/src/truth.xml.preserve 'warg/src/truth.xml' -> 'warg/src/truth.xml.preserve' make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' dh_auto_configure -O--sourcedirectory=warg cd warg && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 0.2.5... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for floor... no checking for pow... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating src/config.h config.status: executing depfiles commands dh_auto_build -O--sourcedirectory=warg cd warg && make -j2 make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' Making all in src make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make all-am make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-data.o `test -f 'data.cpp' || echo './'`data.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rng.o `test -f 'rng.cpp' || echo './'`rng.cpp data.cpp: In constructor ‘weakarg::Data::Data(std::string)’: data.cpp:50:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 50 | }else if(getNumber(tmpname)!=which){ | ~~~~~~~~~~~~~~~~~~^~~~~~~ data.cpp: In member function ‘void weakarg::Data::subset(std::vector, int)’: data.cpp:169:14: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 169 | if (num<=0 &&seed>=0 || num<0) return; | ~~~~~~~^~~~~~~~~ data.cpp:177:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 177 | for(int i=0;i=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<, int>::value_type’ {aka ‘int’} and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 177 | for(int i=0;i=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<otherChild(origfather,which); | ^~~~~~~~~~~~ moveregraftclonal.cpp: In member function ‘void weakarg::MoveRegraftClonal::regraft(int, int)’: moveregraftclonal.cpp:157:61: warning: unused variable ‘wnode’ [-Wunused-variable] 157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto); | ^~~~~ moveregraftclonal.cpp:157:93: warning: unused variable ‘wtonode’ [-Wunused-variable] 157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto); | ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moverho.o `test -f 'moverho.cpp' || echo './'`moverho.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movescaletree.o `test -f 'movescaletree.cpp' || echo './'`movescaletree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movegreedytree.o `test -f 'movegreedytree.cpp' || echo './'`movegreedytree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp movegreedytree.cpp: In member function ‘void weakarg::MoveGreedyTree::applyChanges(std::vector)’: movegreedytree.cpp:230:26: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 230 | int whichto=-1,tmp; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-mpiutils.o `test -f 'mpiutils.cpp' || echo './'`mpiutils.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-node.o `test -f 'node.cpp' || echo './'`node.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-param.o `test -f 'param.cpp' || echo './'`param.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-recedge.o `test -f 'recedge.cpp' || echo './'`recedge.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rectree.o `test -f 'rectree.cpp' || echo './'`rectree.cpp rectree.cpp: In member function ‘int weakarg::RecTree::moveNodeTime(int, int*, double, int, std::vector*, std::vector*)’: rectree.cpp:1112:14: warning: variable ‘newfather’ set but not used [-Wunused-but-set-variable] 1112 | int newfather,notnewfather; | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-tree.o `test -f 'tree.cpp' || echo './'`tree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp weakarg.cpp:40:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 40 | ret.append(__DATE__); | ^~~~~~~~ weakarg.cpp:42:20: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 42 | ret.append(__TIME__); | ^~~~~~~~ weakarg.cpp: In function ‘int main(int, char**)’: weakarg.cpp:127:10: warning: variable ‘setregions’ set but not used [-Wunused-but-set-variable] 127 | bool setregions=false; | ^~~~~~~~~~ weakarg.cpp: In function ‘std::vector weakarg::readInputFiles(Data*&, RecTree*&, std::vector&, std::vector&, std::vector&, std::vector >, std::string, int)’: weakarg.cpp:342:14: warning: variable ‘setregions’ set but not used [-Wunused-but-set-variable] 342 | bool setregions=false; | ^~~~~~~~~~ weakarg.cpp: In function ‘bool weakarg::initializeTree(Data*&, RecTree*&, std::vector >, std::string)’: weakarg.cpp:404:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]); | ^~ weakarg.cpp:404:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]); | ^ g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-RikKKw/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wl,-z,relro -Wl,-z,now -o warg warg-data.o warg-rng.o warg-wargxml.o warg-move.o warg-metropolis.o warg-moveaddedge.o warg-moveageclonal.o warg-movedelta.o warg-moveedgechange.o warg-moveregraftclonal.o warg-moveremedge.o warg-moverho.o warg-movescaletree.o warg-movegreedytree.o warg-movesitechange.o warg-movetheta.o warg-movetimechange.o warg-mpiutils.o warg-node.o warg-param.o warg-recedge.o warg-rectree.o warg-tree.o warg-weakarg.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' Making all in scripts make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' dh_auto_test -O--sourcedirectory=warg cd warg && make -j2 check "TESTSUITEFLAGS=-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' Making check in src make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make profilerun.sh make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[3]: 'profilerun.sh' is up to date. make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make check-TESTS make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[4]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' PASS: profilerun.sh ============================================================================ Testsuite summary for clonalorigin 0.0.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' Making check in scripts make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=warg dh_prep -O--sourcedirectory=warg dh_auto_install --destdir=debian/clonalorigin/ -O--sourcedirectory=warg cd warg && make -j2 install DESTDIR=/build/clonalorigin-RikKKw/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' Making install in src make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-RikKKw/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c warg '/build/clonalorigin-RikKKw/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/src' Making install in scripts make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-RikKKw/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/clonalorigin-RikKKw/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[3]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[2]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0/warg' debian/rules override_dh_install make[1]: Entering directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' dh_install rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl make[1]: Leaving directory '/build/clonalorigin-RikKKw/clonalorigin-1.0' dh_installdocs -O--sourcedirectory=warg dh_installchangelogs -O--sourcedirectory=warg dh_installman -O--sourcedirectory=warg dh_installsystemduser -O--sourcedirectory=warg dh_lintian -O--sourcedirectory=warg dh_perl -O--sourcedirectory=warg dh_link -O--sourcedirectory=warg dh_strip_nondeterminism -O--sourcedirectory=warg dh_compress -O--sourcedirectory=warg dh_fixperms -O--sourcedirectory=warg dh_missing -O--sourcedirectory=warg dh_dwz -a -O--sourcedirectory=warg dh_strip -a -O--sourcedirectory=warg dh_makeshlibs -a -O--sourcedirectory=warg dh_shlibdeps -a -O--sourcedirectory=warg dh_installdeb -O--sourcedirectory=warg dh_gencontrol -O--sourcedirectory=warg dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=warg dh_builddeb -O--sourcedirectory=warg dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-8_amd64.deb'. dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-8_amd64.deb'. dpkg-genbuildinfo -O../clonalorigin_1.0-8_amd64.buildinfo dpkg-genchanges -O../clonalorigin_1.0-8_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 2025-08-17T09:53:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 17 Aug 2025 09:53:42 +0000 | +------------------------------------------------------------------------------+ clonalorigin_1.0-8_amd64.changes: --------------------------------- Format: 1.8 Date: Fri, 29 Dec 2023 13:11:47 +0100 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: source amd64 Version: 1.0-8 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: clonalorigin - inference of homologous recombination in bacteria using whole gen Closes: 884475 Changes: clonalorigin (1.0-8) unstable; urgency=medium . * shorten-test.patch: new: reduce stress on buildds. (Closes: #884475) * d/tests/: new: add autopkgtest. * clonalorigin-gui.1: minor fixups. * d/blocksplit.1: new: document upstream script. * d/computeMedians.1: new: document upstream script. * d/makeMauveWargFile.1: new: document upstream script. * d/clonalorigin-gui.1: minor fixup. * d/warg.1: minor fixup in description. * d/clonalorigin.1: remove: unused. The real manual page in the binary package is a link to warg(1). * d/clonalorigin.manpages: add missing script manuals. * d/control: recommend libxml-parser-perl. This library is needed by computeMedians, although it does not seem critical to typical clonalorigin workloads. * d/*lintian-overrides: new: flag a false positive. Checksums-Sha1: 1cff182ea198188f5008c2755ced5d98a65be903 1155 clonalorigin_1.0-8.dsc 8b84785b3d7ffb55e62b2b9932c4c62ec9900f03 10608 clonalorigin_1.0-8.debian.tar.xz 8cae8fe9558e89d9681952904f9c959f835652b8 1760132 clonalorigin-dbgsym_1.0-8_amd64.deb 808bf0a2b277ca2471a35885270baa23a00f335c 5252 clonalorigin_1.0-8_amd64.buildinfo 327a8acdc4eeab1fb5eb05801e54c10f65afc251 178032 clonalorigin_1.0-8_amd64.deb Checksums-Sha256: d1e934a6db31bb32fea17496d489759bcb364d561401441a7543bfa9e9992de5 1155 clonalorigin_1.0-8.dsc 192e0da0642eea3f9e86d40b535ac89c900be9cfe557d163ca29a54e7f479882 10608 clonalorigin_1.0-8.debian.tar.xz a0ddb192e5279c179a36dace1edd33153665024dd4c512d5c727fa4b80b054ef 1760132 clonalorigin-dbgsym_1.0-8_amd64.deb 213569fa6456109311a8a02ee24b3084169f14c4c24cbb23855c9e423215acc4 5252 clonalorigin_1.0-8_amd64.buildinfo 9e2ba63958fc7e832647a1683e161b24b6b438bb5be33fdc60443caf5f1dc3b3 178032 clonalorigin_1.0-8_amd64.deb Files: 003253fed02793d604968b7fb330c622 1155 science optional clonalorigin_1.0-8.dsc 905b8b38da217ad00e12e9f849ec267d 10608 science optional clonalorigin_1.0-8.debian.tar.xz 2cb0c2b3a25faf9a8c745a0fe82d5363 1760132 debug optional clonalorigin-dbgsym_1.0-8_amd64.deb adb706d18a0b3291bb5af654299df58d 5252 science optional clonalorigin_1.0-8_amd64.buildinfo c307a0d4c821c0ee0fa3b063078a94e4 178032 science optional clonalorigin_1.0-8_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 17 Aug 2025 09:53:42 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: amd64 source Version: 1.0-8 Checksums-Md5: 003253fed02793d604968b7fb330c622 1155 clonalorigin_1.0-8.dsc 2cb0c2b3a25faf9a8c745a0fe82d5363 1760132 clonalorigin-dbgsym_1.0-8_amd64.deb c307a0d4c821c0ee0fa3b063078a94e4 178032 clonalorigin_1.0-8_amd64.deb Checksums-Sha1: 1cff182ea198188f5008c2755ced5d98a65be903 1155 clonalorigin_1.0-8.dsc 8cae8fe9558e89d9681952904f9c959f835652b8 1760132 clonalorigin-dbgsym_1.0-8_amd64.deb 327a8acdc4eeab1fb5eb05801e54c10f65afc251 178032 clonalorigin_1.0-8_amd64.deb Checksums-Sha256: d1e934a6db31bb32fea17496d489759bcb364d561401441a7543bfa9e9992de5 1155 clonalorigin_1.0-8.dsc a0ddb192e5279c179a36dace1edd33153665024dd4c512d5c727fa4b80b054ef 1760132 clonalorigin-dbgsym_1.0-8_amd64.deb 9e2ba63958fc7e832647a1683e161b24b6b438bb5be33fdc60443caf5f1dc3b3 178032 clonalorigin_1.0-8_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 17 Aug 2025 09:53:42 +0000 Build-Path: /build/clonalorigin-RikKKw/clonalorigin-1.0 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 (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libblkid1 (= 2.41.1-1), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.192-4), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libgsl-dev (= 2.8+dfsg-5), libgsl28 (= 2.8+dfsg-5), libgslcblas0 (= 2.8+dfsg-5), libhwasan0 (= 15.2.0-1), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41.1-1), liblsan0 (= 15.2.0-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-1), 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), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libquadmath0 (= 15.2.0-1), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-4), libsmartcols1 (= 2.41.1-1), libsqlite3-0 (= 3.46.1-7), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libsystemd0 (= 258~rc2-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 258~rc2-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-1), libxml2-16 (= 2.14.5+dfsg-0.1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), 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 (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), po-debconf (= 1.0.21+nmu1), rename (= 2.02-1), 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 (= 2.41.1-1), 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="1703851907" +------------------------------------------------------------------------------+ | Package contents Sun, 17 Aug 2025 09:53:43 +0000 | +------------------------------------------------------------------------------+ clonalorigin-dbgsym_1.0-8_amd64.deb ----------------------------------- new Debian package, version 2.0. size 1760132 bytes: control archive=536 bytes. 387 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: clonalorigin-dbgsym Source: clonalorigin Version: 1.0-8 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1828 Depends: clonalorigin (= 1.0-8) Section: debug Priority: optional Description: debug symbols for clonalorigin Build-Ids: 5d62aace06c0e55a353e549d4ce30dfbb6c640e8 drwxr-xr-x root/root 0 2023-12-29 12:11 ./ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/lib/debug/.build-id/5d/ -rw-r--r-- root/root 1860936 2023-12-29 12:11 ./usr/lib/debug/.build-id/5d/62aace06c0e55a353e549d4ce30dfbb6c640e8.debug drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/ lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/share/doc/clonalorigin-dbgsym -> clonalorigin clonalorigin_1.0-8_amd64.deb ---------------------------- new Debian package, version 2.0. size 178032 bytes: control archive=1300 bytes. 1108 bytes, 21 lines control 800 bytes, 12 lines md5sums Package: clonalorigin Version: 1.0-8 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 453 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgsl28 (>= 2.8+dfsg), libstdc++6 (>= 14) Recommends: libxml-parserl-perl Section: science Priority: optional Homepage: https://github.com/xavierdidelot/clonalorigin Description: inference of homologous recombination in bacteria using whole genome sequences Bacteria, unlike us, can reproduce on their own. They do however have mechanisms that transfer DNA between organisms, a process more formally known as recombination. The mechanisms by which recombination takes place have been studied extensively in the laboratory but much remains to be understood concerning how, when and where recombination takes place within natural populations of bacteria and how it helps them to adapt to new environments. ClonalOrigin performs a comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. drwxr-xr-x root/root 0 2023-12-29 12:11 ./ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/bin/ -rwxr-xr-x root/root 430 2023-12-29 12:11 ./usr/bin/blocksplit lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/bin/clonalorigin -> warg -rwxr-xr-x root/root 3039 2023-12-29 12:11 ./usr/bin/computeMedians -rwxr-xr-x root/root 1111 2023-12-29 12:11 ./usr/bin/makeMauveWargFile -rwxr-xr-x root/root 433568 2023-12-29 12:11 ./usr/bin/warg drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/doc/clonalorigin/ -rw-r--r-- root/root 504 2023-12-29 12:11 ./usr/share/doc/clonalorigin/README.Debian -rw-r--r-- root/root 1061 2023-12-29 12:11 ./usr/share/doc/clonalorigin/changelog.Debian.gz -rw-r--r-- root/root 542 2023-12-29 12:11 ./usr/share/doc/clonalorigin/copyright drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 124 2023-12-29 12:11 ./usr/share/lintian/overrides/clonalorigin drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/man/ drwxr-xr-x root/root 0 2023-12-29 12:11 ./usr/share/man/man1/ -rw-r--r-- root/root 529 2023-12-29 12:11 ./usr/share/man/man1/blocksplit.1.gz lrwxrwxrwx root/root 0 2023-12-29 12:11 ./usr/share/man/man1/clonalorigin.1.gz -> warg.1.gz -rw-r--r-- root/root 423 2023-12-29 12:11 ./usr/share/man/man1/computeMedians.1.gz -rw-r--r-- root/root 421 2023-12-29 12:11 ./usr/share/man/man1/makeMauveWargFile.1.gz -rw-r--r-- root/root 1602 2023-12-29 12:11 ./usr/share/man/man1/warg.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 17 Aug 2025 09:53:43 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 17 Aug 2025 09:53:43 +0000 | +------------------------------------------------------------------------------+ Purging /build/clonalorigin-RikKKw Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 17 Aug 2025 09:53:44 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 31644 Build-Time: 110 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/clonalorigin_1.0-8.dsc Machine Architecture: amd64 Package: clonalorigin Package-Time: 131 Source-Version: 1.0-8 Space: 31644 Status: successful Version: 1.0-8 -------------------------------------------------------------------------------- Finished at 2025-08-17T09:53:42Z Build needed 00:02:11, 31644k disk space