sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | clonalorigin 1.0-9 (amd64) Thu, 09 Jul 2026 05:08:19 +0000 | +==============================================================================+ Package: clonalorigin Version: 1.0-9 Source Version: 1.0-9 Distribution: perl-5.44-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 Thu, 09 Jul 2026 05:08:20 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-9 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup clonalorigin_1.0-9 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 09 Jul 2026 05:08:21 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] 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 Thu, 09 Jul 2026 05:08:22 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/clonalorigin_1.0-9.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 09 Jul 2026 05:08:23 +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-NF3qcT/resolver-b3fccy/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/apt_archive ./ InRelease Get:2 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/apt_archive ./ Release [609 B] Ign:3 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/apt_archive ./ Release.gpg Get:4 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/apt_archive ./ Sources [620 B] Get:5 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/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 python3:any 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 14.3 MB of archives. After this operation, 66.0 MB of additional disk space will be used. Get:1 copy:/build/clonalorigin-NF3qcT/resolver-b3fccy/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 1:5.47-4 [345 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 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 1.4.21-1 [332 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [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 1.15.1-1 [17.1 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 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 14.3 [934 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-6+b1 [131 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-6+b1 [1002 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-6+b1 [1248 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-2 [19.9 kB] Preconfiguring packages ... Fetched 14.3 MB in 0s (141 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14518 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%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-3_amd64.deb ... Unpacking gettext-base (1.0-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... 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Selecting previously unselected package rename. Preparing to unpack .../31-rename_2.02-2_all.deb ... Unpacking rename (2.02-2) ... 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 (1.5.8-3) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libgslcblas0:amd64 (2.8+dfsg-6+b1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.3) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up gettext-base (1.0-3) ... Setting up m4 (1.4.21-1) ... Setting up rename (2.02-2) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up autopoint (1.0-3) ... Setting up autoconf (2.73-2) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libgsl28:amd64 (2.8+dfsg-6+b1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libgsl-dev (2.8+dfsg-6+b1) ... Setting up libtool (2.5.4-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... 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 (14.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 09 Jul 2026 05:08:29 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Thu, 09 Jul 2026 05:08:29 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgsl-dev_2.8+dfsg-6+b1 libgsl28_2.8+dfsg-6+b1 libgslcblas0_2.8+dfsg-6+b1 libhogweed6t64_3.10.2-1+b1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libksba8_1.8.0-3 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-3+b2 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.2-4 po-debconf_1.0.22 readline-common_8.3-4 rename_2.02-2 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 09 Jul 2026 05:08:29 +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-NF3qcT/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 clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Thu, 09 Jul 2026 05:08:30 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-9 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network clonalorigin_1.0-9 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/clonalorigin-NF3qcT/clonalorigin-1.0 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-04df3bba-0268-4d97-b794-4fae08c8d8e5 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-NF3qcT/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-NF3qcT/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 autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: configure.ac: creating directory config autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:58: warning: The macro 'AC_TRY_RUN' is obsolete. configure.ac:58: You should run autoupdate. ./lib/autoconf/general.m4:3053: 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.m4:2976: AC_TRY_LINK is expanded from... m4/gsl.m4:5: AX_PATH_GSL is expanded from... configure.ac:58: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing 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' autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' debian/rules execute_before_dh_auto_configure make[1]: Entering directory '/build/clonalorigin-NF3qcT/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-NF3qcT/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 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 x86_64-linux-gnu-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-linux-gnu-g++... none checking for gcc... x86_64-linux-gnu-gcc checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-linux-gnu-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-NF3qcT/clonalorigin-1.0/warg' Making all in src make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make all-am make[3]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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); | ^~~~~~~~~~~~ x86_64-linux-gnu-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-NF3qcT/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp 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); | ^~~~~~~ x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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; | ^~~ x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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; | ^~~~~~~~~ x86_64-linux-gnu-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-NF3qcT/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 x86_64-linux-gnu-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-NF3qcT/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]); | ^ x86_64-linux-gnu-g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-NF3qcT/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-NF3qcT/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' Making all in scripts make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-NF3qcT/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-NF3qcT/clonalorigin-1.0/warg' Making check in src make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make profilerun.sh make[3]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[3]: 'profilerun.sh' is up to date. make[3]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make check-TESTS make[3]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[4]: Entering directory '/build/clonalorigin-NF3qcT/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-NF3qcT/clonalorigin-1.0/warg/src' make[3]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' Making check in scripts make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-NF3qcT/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-NF3qcT/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' Making install in src make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[3]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-NF3qcT/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c warg '/build/clonalorigin-NF3qcT/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/src' Making install in scripts make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[3]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/clonalorigin-NF3qcT/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/clonalorigin-NF3qcT/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[3]: Entering directory '/build/clonalorigin-NF3qcT/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-NF3qcT/clonalorigin-1.0/warg' make[2]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0/warg' debian/rules override_dh_install make[1]: Entering directory '/build/clonalorigin-NF3qcT/clonalorigin-1.0' dh_install rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl make[1]: Leaving directory '/build/clonalorigin-NF3qcT/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_1.0-9_amd64.deb'. dpkg-deb: building package 'clonalorigin' in '../clonalorigin_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 2026-07-09T05:09:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 09 Jul 2026 05:09:55 +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-5.44-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 834aa5ea1484c4069d6ab0d4c45a1a2031a88dcd 1683636 clonalorigin-dbgsym_1.0-9_amd64.deb ef11394a52972b00b639def9229e662f2a2336ab 5327 clonalorigin_1.0-9_amd64.buildinfo 6343eb8fd67cd228b7ed0a4c86d4904ee4fd22ff 173456 clonalorigin_1.0-9_amd64.deb Checksums-Sha256: 1fd4e2e76e962e1555582c75772f1223957c257ecc4d462d206b42f79894000d 1155 clonalorigin_1.0-9.dsc bc5d7358e8a545d9af46101d285651b7323df123b9c71b701d4189ec16015a92 10684 clonalorigin_1.0-9.debian.tar.xz 4a431375d5f0e96d963a00d668e21bc2ba240eddc63b34cdfb1eedb7cd29914b 1683636 clonalorigin-dbgsym_1.0-9_amd64.deb 204ffeb840bf209102dc90660ceb8faa7480a7a18ed3dc6f8aff5c131cc8a568 5327 clonalorigin_1.0-9_amd64.buildinfo 1395734bdb603378581c5e794ee576f084849b9c66696b34dc6671b63c1e89b6 173456 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 34404278765f1fb2e59ada509ab97458 1683636 debug optional clonalorigin-dbgsym_1.0-9_amd64.deb ad7a759050888e03983b675fc356b312 5327 science optional clonalorigin_1.0-9_amd64.buildinfo 32b1748cfa984dad46e062e29c3330f3 173456 science optional clonalorigin_1.0-9_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Thu, 09 Jul 2026 05:09:55 +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 34404278765f1fb2e59ada509ab97458 1683636 clonalorigin-dbgsym_1.0-9_amd64.deb 32b1748cfa984dad46e062e29c3330f3 173456 clonalorigin_1.0-9_amd64.deb Checksums-Sha1: 0debec6b1de4d733d5fbee1c74b5c70365266178 1155 clonalorigin_1.0-9.dsc 834aa5ea1484c4069d6ab0d4c45a1a2031a88dcd 1683636 clonalorigin-dbgsym_1.0-9_amd64.deb 6343eb8fd67cd228b7ed0a4c86d4904ee4fd22ff 173456 clonalorigin_1.0-9_amd64.deb Checksums-Sha256: 1fd4e2e76e962e1555582c75772f1223957c257ecc4d462d206b42f79894000d 1155 clonalorigin_1.0-9.dsc 4a431375d5f0e96d963a00d668e21bc2ba240eddc63b34cdfb1eedb7cd29914b 1683636 clonalorigin-dbgsym_1.0-9_amd64.deb 1395734bdb603378581c5e794ee576f084849b9c66696b34dc6671b63c1e89b6 173456 clonalorigin_1.0-9_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 09 Jul 2026 05:09:55 +0000 Build-Path: /build/clonalorigin-NF3qcT/clonalorigin-1.0 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgsl-dev (= 2.8+dfsg-6+b1), libgsl28 (= 2.8+dfsg-6+b1), libgslcblas0 (= 2.8+dfsg-6+b1), libhwasan0 (= 16.1.0-2), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), liblsan0 (= 16.1.0-2), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libquadmath0 (= 16.1.0-2), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), po-debconf (= 1.0.22), rename (= 2.02-2), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" 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 Thu, 09 Jul 2026 05:09:55 +0000 | +------------------------------------------------------------------------------+ clonalorigin-dbgsym_1.0-9_amd64.deb ----------------------------------- new Debian package, version 2.0. size 1683636 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: 1749 Depends: clonalorigin (= 1.0-9) Section: debug Priority: optional Description: debug symbols for clonalorigin Build-Ids: f92a673050d1f07f71498a8622f74b5af7033b8b 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/f9/ -rw-r--r-- root/root 1780200 2026-01-03 18:21 ./usr/lib/debug/.build-id/f9/2a673050d1f07f71498a8622f74b5af7033b8b.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 173456 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: 436 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 417184 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 969 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 Thu, 09 Jul 2026 05:09:56 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 09 Jul 2026 05:09:56 +0000 | +------------------------------------------------------------------------------+ Purging /build/clonalorigin-NF3qcT Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 09 Jul 2026 05:09:57 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 31076 Build-Time: 85 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/clonalorigin_1.0-9.dsc Machine Architecture: amd64 Package: clonalorigin Package-Time: 96 Source-Version: 1.0-9 Space: 31076 Status: successful Version: 1.0-9 -------------------------------------------------------------------------------- Finished at 2026-07-09T05:09:55Z Build needed 00:01:36, 31076k disk space