sbuild (Debian sbuild) 0.91.1 (08 October 2025) on carme.larted.org.uk +==============================================================================+ | clonalorigin 1.0-9 (amd64) Sat, 03 Jan 2026 21:04:20 +0000 | +==============================================================================+ Package: clonalorigin Version: 1.0-9 Source Version: 1.0-9 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 Sat, 03 Jan 2026 21:04:21 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-9 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-9 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sat, 03 Jan 2026 21:04:21 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [187 kB] Get:3 http://deb.debian.org/debian sid InRelease [187 kB] Get:4 file:/srv/reprepro perl-5.42/main amd64 Packages [634 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-2026-01-03-2005.57-F-2026-01-03-2005.57.pdiff [21.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2026-01-03-2005.57-F-2026-01-03-2005.57.pdiff [21.9 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-01-03-2005.57-F-2026-01-03-2005.57.pdiff [16.7 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2026-01-03-2005.57-F-2026-01-03-2005.57.pdiff [16.7 kB] Fetched 539 kB in 2s (225 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sat, 03 Jan 2026 21:04:26 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/clonalorigin_1.0-9.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sat, 03 Jan 2026 21:04:26 +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-2pVEC3/resolver-y15vvJ/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/apt_archive ./ InRelease Get:2 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/apt_archive ./ Release [609 B] Ign:3 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/apt_archive ./ Release.gpg Get:4 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/apt_archive ./ Sources [620 B] Get:5 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/apt_archive ./ Packages [659 B] Fetched 1888 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... 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 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 13.3 MB of archives. After this operation, 53.2 MB of additional disk space will be used. Get:1 copy:/build/clonalorigin-2pVEC3/resolver-y15vvJ/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 0.0.26 [27.0 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 0.23.2-1 [245 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-3 [99.1 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 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 1.4.20-2 [325 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 1:1.18.1-3 [878 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.29 [92.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 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 1.0.22 [216 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.29 [943 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5.1 [137 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5.1 [1068 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5.1 [1336 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Preconfiguring packages ... Fetched 13.3 MB in 0s (126 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23331 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... 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_0.23.2-1_amd64.deb ... Unpacking gettext-base (0.23.2-1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-10_amd64.deb ... Unpacking groff-base (1.23.0-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.3-3_amd64.deb ... Unpacking bsdextrautils (2.41.3-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-2) ... 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_1.4.20-2_amd64.deb ... Unpacking m4 (1.4.20-2) ... 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%3a1.18.1-3_all.deb ... Unpacking automake (1:1.18.1-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.2-1_all.deb ... Unpacking autopoint (0.23.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.29_all.deb ... Unpacking libdebhelper-perl (13.29) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-9_all.deb ... Unpacking libtool (2.5.4-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.194-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../23-libxml2-16_2.15.1+dfsg-2+b1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_0.23.2-1_amd64.deb ... Unpacking gettext (0.23.2-1) ... 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_1.0.22_all.deb ... Unpacking po-debconf (1.0.22) ... Selecting previously unselected package debhelper. Preparing to unpack .../27-debhelper_13.29_all.deb ... Unpacking debhelper (13.29) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../28-libgslcblas0_2.8+dfsg-5.1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl28:amd64. Preparing to unpack .../29-libgsl28_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl28:amd64 (2.8+dfsg-5.1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../30-libgsl-dev_2.8+dfsg-5.1_amd64.deb ... Unpacking libgsl-dev (2.8+dfsg-5.1) ... 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 (1.5.8-2) ... Setting up bsdextrautils (2.41.3-3) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5.1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Setting up libdebhelper-perl (13.29) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.2-1) ... Setting up m4 (1.4.20-2) ... 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 (0.194-1) ... Setting up autotools-dev (20240727.1) ... Setting up autopoint (0.23.2-1) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libgsl28:amd64 (2.8+dfsg-5.1) ... Setting up automake (1:1.18.1-3) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.2-1) ... Setting up libgsl-dev (2.8+dfsg-5.1) ... Setting up libtool (2.5.4-9) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.29) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-6) ... +------------------------------------------------------------------------------+ | Check architectures Sat, 03 Jan 2026 21:04:30 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sat, 03 Jan 2026 21:04:30 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.16.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.16.5-1 (2025-09-05) amd64 (x86_64) Toolchain package versions: binutils_2.45.50.20251209-1 dpkg-dev_1.23.3 g++-14_14.3.0-10 g++-15_15.2.0-12 gcc-14_14.3.0-10 gcc-15_15.2.0-12 libc6-dev_2.42-6 libstdc++-14-dev_14.3.0-10 libstdc++-15-dev_15.2.0-12 libstdc++6_15.2.0-12 linux-libc-dev_6.17.13-1 Package versions: adduser_3.154 apt_3.1.12 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45.50.20251209-1 binutils-common_2.45.50.20251209-1 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.45.50.20251209-1 bsdextrautils_2.41.3-3 bsdutils_1:2.41.3-3 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-14_14.3.0-10 cpp-14-x86-64-linux-gnu_14.3.0-10 cpp-15_15.2.0-12 cpp-15-x86-64-linux-gnu_15.2.0-12 cpp-x86-64-linux-gnu_4:15.2.0-4 dash_0.5.12-12 debconf_1.5.91 debhelper_13.29 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.8-5 dpkg_1.23.3 dpkg-dev_1.23.3 dwz_0.16-2 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-14_14.3.0-10 g++-14-x86-64-linux-gnu_14.3.0-10 g++-15_15.2.0-12 g++-15-x86-64-linux-gnu_15.2.0-12 g++-x86-64-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-14_14.3.0-10 gcc-14-base_14.3.0-10 gcc-14-x86-64-linux-gnu_14.3.0-10 gcc-15_15.2.0-12 gcc-15-base_15.2.0-12 gcc-15-x86-64-linux-gnu_15.2.0-12 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.2-1 gettext-base_0.23.2-1 gnupg_2.4.8-5 gnupg-l10n_2.4.8-5 gpg_2.4.8-5 gpg-agent_2.4.8-5 gpgconf_2.4.8-5 gpgsm_2.4.8-5 grep_3.12-1 groff-base_1.23.0-10 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_3.1.12 libarchive-zip-perl_1.68-1 libasan8_15.2.0-12 libassuan9_3.0.2-2 libatomic1_15.2.0-12 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.45.50.20251209-1 libblkid1_2.41.3-3 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.42-6 libc-dev-bin_2.42-6 libc-gconv-modules-extra_2.42-6 libc-l10n_2.42-6 libc6_2.42-6 libc6-dev_2.42-6 libcap-ng0_0.8.5-4+b2 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-12 libcrypt-dev_1:4.5.1-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.45.50.20251209-1 libctf0_2.45.50.20251209-1 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.29 libdpkg-perl_1.23.3 libeatmydata1_131-2+b1 libelf1t64_0.194-1 libffi8_3.5.2-3 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-14-dev_14.3.0-10 libgcc-15-dev_15.2.0-12 libgcc-s1_15.2.0-12 libgcrypt20_1.11.2-3 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.11-3 libgomp1_15.2.0-12 libgpg-error0_1.58-1 libgprofng0_2.45.50.20251209-1 libgsl-dev_2.8+dfsg-5.1 libgsl28_2.8+dfsg-5.1 libgslcblas0_2.8+dfsg-5.1 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-12 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-12 libjansson4_2.14-2+b4 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.3-3 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-12 liblz4-1_1.10.0-6 liblzma5_5.8.2-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.3-3 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1 libnpth0t64_1.8-3 libp11-kit0_0.25.10-1 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_10.46-1 libperl5.40_5.40.1-7 libperl5.42_5.42.0-3 libpipeline1_1.5.8-2 libquadmath0_15.2.0-12 libreadline8t64_8.3-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsemanage-common_3.9-1 libsemanage2_3.9-1+b1 libsepol2_3.9-2 libsframe2_2.45.50.20251209-1 libsmartcols1_2.41.3-3 libsqlite3-0_3.46.1-8 libssl3t64_3.5.4-1 libstdc++-14-dev_14.3.0-10 libstdc++-15-dev_15.2.0-12 libstdc++6_15.2.0-12 libsystemd0_259-1 libtasn1-6_4.20.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_15.2.0-12 libubsan1_15.2.0-12 libuchardet0_0.0.8-2 libudev1_259-1 libunistring5_1.3-2 libuuid1_2.41.3-3 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.13-1 locales-all_2.42-6 login.defs_1:4.18.0-2 m4_1.4.20-2 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20250131-2 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 openssl-provider-legacy_3.5.4-1 passwd_1:4.18.0-2 patch_2.8-2 perl_5.42.0-3 perl-base_5.42.0-3 perl-modules-5.40_5.40.1-7 perl-modules-5.42_5.42.0-3 pinentry-curses_1.3.2-3 po-debconf_1.0.22 readline-common_8.3-3 rename_2.02-1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-5 sysvinit-utils_3.15-6 tar_1.35+dfsg-3.1 util-linux_2.41.3-3 xz-utils_5.8.2-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b2 +------------------------------------------------------------------------------+ | Build Sat, 03 Jan 2026 21:04:30 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: clonalorigin Binary: clonalorigin Architecture: any Version: 1.0-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/xavierdidelot/clonalorigin Standards-Version: 4.7.3 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 42106888edfa2e715196d8f03ed05ed8861101d6 10680 clonalorigin_1.0-9.debian.tar.xz Checksums-Sha256: 73962415160b8b496c81d3e9cbbf68f76c02caf4dd6b41860f01d493b71c6e3a 185865 clonalorigin_1.0.orig.tar.gz f9ec886d55c42163949368b3457dc32eb1386eb61bba6bcfdef1ab449964142d 10680 clonalorigin_1.0-9.debian.tar.xz Files: 310a0c5714e7629c052ab4da50c90f44 185865 clonalorigin_1.0.orig.tar.gz 43f9e4249cfaba3b7f84c084d7a0c63d 10680 clonalorigin_1.0-9.debian.tar.xz Dgit: e031b5abd42e0b362e77001266498831fb6cbb30 debian archive/debian/1.0-9 https://git.dgit.debian.org/clonalorigin -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmlZZjEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpHTQ/5Ae9Z6k/Nz9IVrkMb1cWUuIa63wQY BzyPS3jwJBVipOSoUYzrn2skmgzk185MHxXrr5+IpvGMdfMgqqFY6clWinqwi9yW zoC9klcveE3crkJlWjJ3j1cIOZBgV7Si3cVmBXtsaqDeaWelnnGjm9izflmlUGXu jIZTHnv9NRDdgVHHHoPEcS1nvpmGX2y6geQUuEYZJutkx31MqNllLAzgnOc9/F/q FoNs5YMXC+X13B7JIuDLkYBrpSLs/umaCEwqKbNjsmwAMNl5GjdfvRedIKmh63D3 RbUx4pY7kS/46MWoJGPe327ScwwYnhQhdlDChlLdx53oZlUAmjjRR/gJxdDU/qQE brgB8VZoJvwC2HVKjXfNhvqSaGHFKnjeXldQZxlkK0WP+OX1YOcELeso1dplo1yV 4tIisYvHtodpqgpdqQy2Kr6Coj+ixGE9pcW0Gtnjhjdy+YF1LLVXSf2FQxnSBZqJ R4rdHwXyOK178fNUHhaNVAsZGfHPztyMUicwZTokE3yOEDzO89paz9G0Ev2otCj3 8tlsC/9/XFX6OUiTpv6jLASjV1j0MWqq9LkQMFsWJ0BHsOePXMu08CY/pKfIkuz3 /GyGAGvYXD+kalF/a8M1NaqDuA2jkFH/xV7qIJBBc7cUnGSkRvbc+oa7tGRvnc/J oHhMbVofwKp04Fo= =MFDA -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-9.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./clonalorigin_1.0-9.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting clonalorigin in /build/clonalorigin-2pVEC3/clonalorigin-1.0 dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz dpkg-source: info: unpacking clonalorigin_1.0-9.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 Sat, 03 Jan 2026 21:04:31 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-9 perl-5.42-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-9 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-2pVEC3/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-f611065a-d320-4647-a871-a416df89dc67 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 1.0-9 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-2pVEC3/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-2pVEC3/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_1.0-9.debian.tar.xz dpkg-source: info: building clonalorigin in clonalorigin_1.0-9.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-2pVEC3/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-2pVEC3/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 whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar 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-2pVEC3/clonalorigin-1.0/warg' Making all in src make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make all-am make[3]: Entering directory '/build/clonalorigin-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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-2pVEC3/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 -fcf-protection -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-2pVEC3/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' Making all in scripts make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-2pVEC3/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-2pVEC3/clonalorigin-1.0/warg' Making check in src make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make profilerun.sh make[3]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[3]: 'profilerun.sh' is up to date. make[3]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make check-TESTS make[3]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[4]: Entering directory '/build/clonalorigin-2pVEC3/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-2pVEC3/clonalorigin-1.0/warg/src' make[3]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' Making check in scripts make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-2pVEC3/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-2pVEC3/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' Making install in src make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[3]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-2pVEC3/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c warg '/build/clonalorigin-2pVEC3/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/src' Making install in scripts make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[3]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-2pVEC3/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/clonalorigin-2pVEC3/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[3]: Entering directory '/build/clonalorigin-2pVEC3/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-2pVEC3/clonalorigin-1.0/warg' make[2]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0/warg' debian/rules override_dh_install make[1]: Entering directory '/build/clonalorigin-2pVEC3/clonalorigin-1.0' dh_install rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl make[1]: Leaving directory '/build/clonalorigin-2pVEC3/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' in '../clonalorigin_1.0-9_amd64.deb'. dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-9_amd64.deb'. dpkg-genbuildinfo -O../clonalorigin_1.0-9_amd64.buildinfo dpkg-genchanges -O../clonalorigin_1.0-9_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 2026-01-03T21:05:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sat, 03 Jan 2026 21:05:58 +0000 | +------------------------------------------------------------------------------+ clonalorigin_1.0-9_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 03 Jan 2026 19:21:57 +0100 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: source amd64 Version: 1.0-9 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: 1112565 Changes: clonalorigin (1.0-9) unstable; urgency=medium . * d/control: fix typo in Recemmends field. Thanks to Carles Pina i Estany (Closes: #1112565) * d/control: drop redundant Priority: optional. * d/control: drop redundant Rules-Requires-Root: no. * d/control: declare compliance to standards version 4.7.3. * d/watch: convert to v5 Github template. * d/patches/*: normalize Last-Update timestamps. Checksums-Sha1: 0debec6b1de4d733d5fbee1c74b5c70365266178 1155 clonalorigin_1.0-9.dsc 95be2521a8101cc1ec5d339b66e37d2dc0f4f1c7 10684 clonalorigin_1.0-9.debian.tar.xz 6fc83293b867d1594f85eff134fe449e69af95f7 1694432 clonalorigin-dbgsym_1.0-9_amd64.deb 9b4bcf431a7b0162047e845e5b84d8608a55f373 5489 clonalorigin_1.0-9_amd64.buildinfo 3333a31576939121a3f916c78f3b110a8317b33a 175236 clonalorigin_1.0-9_amd64.deb Checksums-Sha256: 1fd4e2e76e962e1555582c75772f1223957c257ecc4d462d206b42f79894000d 1155 clonalorigin_1.0-9.dsc bc5d7358e8a545d9af46101d285651b7323df123b9c71b701d4189ec16015a92 10684 clonalorigin_1.0-9.debian.tar.xz 0c1280c246ab3da691c27171c121ead0b3a986b1ebf64e32bbcc4eeed292ee33 1694432 clonalorigin-dbgsym_1.0-9_amd64.deb d4fc3a0fd3b7d2e5c5175d45f04af895865655eb130acfdb50c7d347c11d5701 5489 clonalorigin_1.0-9_amd64.buildinfo 3342d5ac5411d6b1818fd441e71a9ca6c3c8cfcfc3e5085ef57ccf413e03cace 175236 clonalorigin_1.0-9_amd64.deb Files: 2e15832f7c661f9f85f8916bf6bef3e2 1155 science optional clonalorigin_1.0-9.dsc c544397710fc89c4299e2cab81bb903d 10684 science optional clonalorigin_1.0-9.debian.tar.xz 9ab5558de0b16ea0348127ce3c980681 1694432 debug optional clonalorigin-dbgsym_1.0-9_amd64.deb 3ecba56e3f6721dc94a87c0db617ed3c 5489 science optional clonalorigin_1.0-9_amd64.buildinfo 2f8ccffd7bf8084e0603b38561014fed 175236 science optional clonalorigin_1.0-9_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sat, 03 Jan 2026 21:05:58 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: amd64 source Version: 1.0-9 Checksums-Md5: 2e15832f7c661f9f85f8916bf6bef3e2 1155 clonalorigin_1.0-9.dsc 9ab5558de0b16ea0348127ce3c980681 1694432 clonalorigin-dbgsym_1.0-9_amd64.deb 2f8ccffd7bf8084e0603b38561014fed 175236 clonalorigin_1.0-9_amd64.deb Checksums-Sha1: 0debec6b1de4d733d5fbee1c74b5c70365266178 1155 clonalorigin_1.0-9.dsc 6fc83293b867d1594f85eff134fe449e69af95f7 1694432 clonalorigin-dbgsym_1.0-9_amd64.deb 3333a31576939121a3f916c78f3b110a8317b33a 175236 clonalorigin_1.0-9_amd64.deb Checksums-Sha256: 1fd4e2e76e962e1555582c75772f1223957c257ecc4d462d206b42f79894000d 1155 clonalorigin_1.0-9.dsc 0c1280c246ab3da691c27171c121ead0b3a986b1ebf64e32bbcc4eeed292ee33 1694432 clonalorigin-dbgsym_1.0-9_amd64.deb 3342d5ac5411d6b1818fd441e71a9ca6c3c8cfcfc3e5085ef57ccf413e03cace 175236 clonalorigin_1.0-9_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 03 Jan 2026 21:05:57 +0000 Build-Path: /build/clonalorigin-2pVEC3/clonalorigin-1.0 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-1), binutils (= 2.45.50.20251209-1), binutils-common (= 2.45.50.20251209-1), binutils-x86-64-linux-gnu (= 2.45.50.20251209-1), bsdextrautils (= 2.41.3-3), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:15.2.0-4), cpp-14 (= 14.3.0-10), cpp-14-x86-64-linux-gnu (= 14.3.0-10), cpp-15 (= 15.2.0-12), cpp-15-x86-64-linux-gnu (= 15.2.0-12), cpp-x86-64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.29), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.3), dpkg-dev (= 1.23.3), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-12), g++-15-x86-64-linux-gnu (= 15.2.0-12), g++-x86-64-linux-gnu (= 4:15.2.0-4), gcc (= 4:15.2.0-4), gcc-14 (= 14.3.0-10), gcc-14-base (= 14.3.0-10), gcc-14-x86-64-linux-gnu (= 14.3.0-10), gcc-15 (= 15.2.0-12), gcc-15-base (= 15.2.0-12), gcc-15-x86-64-linux-gnu (= 15.2.0-12), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1), groff-base (= 1.23.0-10), 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 (= 15.2.0-12), libatomic1 (= 15.2.0-12), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.45.50.20251209-1), libblkid1 (= 2.41.3-3), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.42-6), libc-dev-bin (= 2.42-6), libc-gconv-modules-extra (= 2.42-6), libc6 (= 2.42-6), libc6-dev (= 2.42-6), libcap-ng0 (= 0.8.5-4+b2), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-12), libcrypt-dev (= 1:4.5.1-1), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.45.50.20251209-1), libctf0 (= 2.45.50.20251209-1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.29), libdpkg-perl (= 1.23.3), libelf1t64 (= 0.194-1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-14-dev (= 14.3.0-10), libgcc-15-dev (= 15.2.0-12), libgcc-s1 (= 15.2.0-12), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgmp10 (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-12), libgprofng0 (= 2.45.50.20251209-1), libgsl-dev (= 2.8+dfsg-5.1), libgsl28 (= 2.8+dfsg-5.1), libgslcblas0 (= 2.8+dfsg-5.1), libhwasan0 (= 15.2.0-12), libisl23 (= 0.27-1), libitm1 (= 15.2.0-12), libjansson4 (= 2.14-2+b4), liblsan0 (= 15.2.0-12), liblzma5 (= 5.8.2-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.3-3), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), 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 (= 10.46-1), libperl5.42 (= 5.42.0-3), libpipeline1 (= 1.5.8-2), libquadmath0 (= 15.2.0-12), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsframe2 (= 2.45.50.20251209-1), libsmartcols1 (= 2.41.3-3), libssl3t64 (= 3.5.4-1), libstdc++-15-dev (= 15.2.0-12), libstdc++6 (= 15.2.0-12), libsystemd0 (= 259-1), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-12), libubsan1 (= 15.2.0-12), libuchardet0 (= 0.0.8-2), libudev1 (= 259-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.3-3), libxml2-16 (= 2.15.1+dfsg-2+b1), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.13-1), m4 (= 1.4.20-2), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-2), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.42.0-3), perl-base (= 5.42.0-3), perl-modules-5.42 (= 5.42.0-3), po-debconf (= 1.0.22), rename (= 2.02-1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.3-3), xz-utils (= 5.8.2-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b2) 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" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1767464517" +------------------------------------------------------------------------------+ | Package contents Sat, 03 Jan 2026 21:05:58 +0000 | +------------------------------------------------------------------------------+ clonalorigin-dbgsym_1.0-9_amd64.deb ----------------------------------- new Debian package, version 2.0. size 1694432 bytes: control archive=536 bytes. 387 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: clonalorigin-dbgsym Source: clonalorigin Version: 1.0-9 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 1760 Depends: clonalorigin (= 1.0-9) Section: debug Priority: optional Description: debug symbols for clonalorigin Build-Ids: a6b25f2a87d28fa44c8c1f1e13a11f632bd1f1d6 drwxr-xr-x root/root 0 2026-01-03 18:21 ./ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/lib/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/lib/debug/.build-id/a6/ -rw-r--r-- root/root 1791464 2026-01-03 18:21 ./usr/lib/debug/.build-id/a6/b25f2a87d28fa44c8c1f1e13a11f632bd1f1d6.debug drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-01-03 18:21 ./usr/share/doc/clonalorigin-dbgsym -> clonalorigin clonalorigin_1.0-9_amd64.deb ---------------------------- new Debian package, version 2.0. size 175236 bytes: control archive=1300 bytes. 1107 bytes, 21 lines control 800 bytes, 12 lines md5sums Package: clonalorigin Version: 1.0-9 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 441 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgsl28 (>= 2.8+dfsg), libstdc++6 (>= 14) Recommends: libxml-parser-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 2026-01-03 18:21 ./ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/bin/ -rwxr-xr-x root/root 430 2026-01-03 18:21 ./usr/bin/blocksplit lrwxrwxrwx root/root 0 2026-01-03 18:21 ./usr/bin/clonalorigin -> warg -rwxr-xr-x root/root 3039 2026-01-03 18:21 ./usr/bin/computeMedians -rwxr-xr-x root/root 1111 2026-01-03 18:21 ./usr/bin/makeMauveWargFile -rwxr-xr-x root/root 421352 2026-01-03 18:21 ./usr/bin/warg drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/doc/clonalorigin/ -rw-r--r-- root/root 504 2026-01-03 18:21 ./usr/share/doc/clonalorigin/README.Debian -rw-r--r-- root/root 1221 2026-01-03 18:21 ./usr/share/doc/clonalorigin/changelog.Debian.gz -rw-r--r-- root/root 542 2026-01-03 18:21 ./usr/share/doc/clonalorigin/copyright drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 124 2026-01-03 18:21 ./usr/share/lintian/overrides/clonalorigin drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/man/ drwxr-xr-x root/root 0 2026-01-03 18:21 ./usr/share/man/man1/ -rw-r--r-- root/root 529 2026-01-03 18:21 ./usr/share/man/man1/blocksplit.1.gz lrwxrwxrwx root/root 0 2026-01-03 18:21 ./usr/share/man/man1/clonalorigin.1.gz -> warg.1.gz -rw-r--r-- root/root 423 2026-01-03 18:21 ./usr/share/man/man1/computeMedians.1.gz -rw-r--r-- root/root 421 2026-01-03 18:21 ./usr/share/man/man1/makeMauveWargFile.1.gz -rw-r--r-- root/root 1602 2026-01-03 18:21 ./usr/share/man/man1/warg.1.gz +------------------------------------------------------------------------------+ | Post Build Sat, 03 Jan 2026 21:05:58 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sat, 03 Jan 2026 21:05:58 +0000 | +------------------------------------------------------------------------------+ Purging /build/clonalorigin-2pVEC3 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sat, 03 Jan 2026 21:06:00 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 31212 Build-Time: 87 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 4 Job: /srv/debomatic/incoming/clonalorigin_1.0-9.dsc Machine Architecture: amd64 Package: clonalorigin Package-Time: 98 Source-Version: 1.0-9 Space: 31212 Status: successful Version: 1.0-9 -------------------------------------------------------------------------------- Finished at 2026-01-03T21:05:58Z Build needed 00:01:38, 31212k disk space