sbuild (Debian sbuild) 0.91.1 (08 October 2025) on carme.larted.org.uk +==============================================================================+ | shovill 1.1.0-10 (amd64) Sun, 02 Nov 2025 17:03:25 +0000 | +==============================================================================+ Package: shovill Version: 1.1.0-10 Source Version: 1.1.0-10 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sun, 02 Nov 2025 17:03:26 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup shovill_1.1.0-10 perl-5.42-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup shovill_1.1.0-10 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 02 Nov 2025 17:03:26 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 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-5.42 InRelease [3042 B] Get:4 file:/srv/reprepro perl-5.42/main amd64 Packages [625 kB] 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 Sun, 02 Nov 2025 17:03:28 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/shovill_1.1.0-10.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 02 Nov 2025 17:03:29 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, spades, skesa, megahit Filtered Build-Depends: debhelper-compat (= 13), build-essential, spades, skesa, megahit dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/shovill-unbv12/resolver-EQLpue/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/shovill-unbv12/resolver-EQLpue/apt_archive ./ InRelease Get:2 copy:/build/shovill-unbv12/resolver-EQLpue/apt_archive ./ Release [609 B] Ign:3 copy:/build/shovill-unbv12/resolver-EQLpue/apt_archive ./ Release.gpg Get:4 copy:/build/shovill-unbv12/resolver-EQLpue/apt_archive ./ Sources [643 B] Get:5 copy:/build/shovill-unbv12/resolver-EQLpue/apt_archive ./ Packages [663 B] Fetched 1915 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 bamtools bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools2.5.3 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost-timer1.83.0 libbrotli1 libcom-err2 libcurl3t64-gnutls libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-c++3 libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp1 libssh2-1t64 libssw0 libtool libuchardet0 libxml2-16 libyaml-0-2 m4 man-db media-types megahit ncbi-vdb-data netbase po-debconf procps python3 python3-all python3-joblib python3-minimal python3-packaging python3-yaml python3.13 python3.13-minimal samtools sensible-utils skesa spades tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-joblib-doc python3.13-venv python3.13-doc binfmt-support cwltool Recommended packages: curl | wget | lynx ca-certificates libarchive-cpio-perl krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults python3-numpy python3-psutil python3-pytest The following NEW packages will be installed: autoconf automake autopoint autotools-dev bamtools bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools2.5.3 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost-timer1.83.0 libbrotli1 libcom-err2 libcurl3t64-gnutls libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-c++3 libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib librtmp1 libssh2-1t64 libssw0 libtool libuchardet0 libxml2-16 libyaml-0-2 m4 man-db media-types megahit ncbi-vdb-data netbase po-debconf procps python3 python3-all python3-joblib python3-minimal python3-packaging python3-yaml python3.13 python3.13-minimal samtools sbuild-build-depends-main-dummy sensible-utils skesa spades tzdata 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 36.7 MB of archives. After this operation, 146 MB of additional disk space will be used. 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unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.3 amd64 2.5.3+dfsg-1 [161 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 bamtools amd64 2.5.3+dfsg-1 [194 kB] Get:33 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Get:54 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:57 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:64 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amd64 libngs-c++3 amd64 3.2.1+dfsg-5 [133 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-7 [180 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15+b2 [21.8 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get:79 http://deb.debian.org/debian unstable/main amd64 megahit amd64 1.2.9-6 [1129 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.4.2-5 [216 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-2 [137 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 skesa amd64 2.4.0-6+b2 [571 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 spades amd64 4.0.0+really3.15.5+dfsg-3 [9261 kB] Preconfiguring packages ... Fetched 36.7 MB in 1s (41.9 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 23311 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_amd64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:amd64 (3.13.9-1) ... Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 23645 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... 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Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libmbedcrypto16:amd64 (3.6.4-2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.9-1) ... Setting up libssw0:amd64 (1.1-15+b2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up automake (1:1.18.1-2) ... 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 (0.23.1-2+b1) ... Setting up libtool (2.5.4-7) ... Setting up python3.13 (3.13.9-1) ... Setting up python3 (3.13.7-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up python3-packaging (25.0-1) ... Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up python3-joblib (1.4.2-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up libcurl3t64-gnutls:amd64 (8.17.0~rc3-1) ... Setting up python3-all (3.13.7-1) ... Setting up python3-yaml (6.0.2-2) ... Setting up skesa (2.4.0-6+b2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up megahit (1.2.9-6) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up debhelper (13.28) ... Setting up samtools (1.22.1-1) ... Setting up spades (4.0.0+really3.15.5+dfsg-3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 02 Nov 2025 17:03:39 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 02 Nov 2025 17:03:39 +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_2.45-8 dpkg-dev_1.22.21 g++-14_14.3.0-10 g++-15_15.2.0-7 gcc-14_14.3.0-10 gcc-15_15.2.0-7 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-10 libstdc++-15-dev_15.2.0-7 libstdc++6_15.2.0-7 linux-libc-dev_6.17.6-1 Package versions: adduser_3.153 apt_3.1.11 autoconf_2.72-3.1 automake_1:1.18.1-2 autopoint_0.23.1-2 autotools-dev_20240727.1 bamtools_2.5.3+dfsg-1 base-files_14 base-passwd_3.6.7 bash_5.3-1 binutils_2.45-8 binutils-common_2.45-8 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.45-8 bsdextrautils_2.41.2-4 bsdutils_1:2.41.2-4 build-essential_12.12 bwa_0.7.19-1 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_15.2.0-7 cpp-15-x86-64-linux-gnu_15.2.0-7 cpp-x86-64-linux-gnu_4:15.2.0-4 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 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_2.4.8-4 dpkg_1.22.21 dpkg-dev_1.22.21 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_15.2.0-7 g++-15-x86-64-linux-gnu_15.2.0-7 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_15.2.0-7 gcc-15-base_15.2.0-7 gcc-15-x86-64-linux-gnu_15.2.0-7 gcc-x86-64-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-4 gnupg-l10n_2.4.8-4 gpg_2.4.8-4 gpg-agent_2.4.8-4 gpgconf_2.4.8-4 gpgsm_2.4.8-4 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.11 libarchive-zip-perl_1.68-1 libasan8_15.2.0-7 libassuan9_3.0.2-2 libatomic1_15.2.0-7 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbamtools2.5.3_2.5.3+dfsg-1 libbinutils_2.45-8 libblkid1_2.41.2-4 libboost-iostreams1.83.0_1.83.0-5 libboost-program-options1.83.0_1.83.0-5 libboost-timer1.83.0_1.83.0-5 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc-l10n_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-7 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-8 libctf0_2.45-8 libcurl3t64-gnutls_8.17.0~rc3-1 libdb5.3t64_5.3.28+dfsg2-10 libdebconfclient0_0.280 libdebhelper-perl_13.28 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.194-1 libexpat1_2.7.3-1 libffi8_3.5.2-2 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-14-dev_14.3.0-10 libgcc-15-dev_15.2.0-7 libgcc-s1_15.2.0-7 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.10-3 libgomp1_15.2.0-7 libgpg-error0_1.56-2 libgprofng0_2.45-8 libgssapi-krb5-2_1.21.3-5 libhogweed6t64_3.10.2-1 libhts3t64_1.22.1+ds2-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-7 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-7 libjansson4_2.14-2+b3 libjsoncpp26_1.9.6-4 libk5crypto3_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.2-4 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-7 liblz4-1_1.10.0-6 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmbedcrypto16_3.6.4-2 libmbedtls21_3.6.4-2 libmbedx509-7_3.6.4-2 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncbi-vdb3_3.2.1+dfsg-2 libncurses6_6.5+20250216-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libngs-c++3_3.2.1+dfsg-5 libngtcp2-16_1.16.0-1 libngtcp2-crypto-gnutls8_1.16.0-1 libnlopt0_2.7.1-7 libnpth0t64_1.8-3 libp11-kit0_0.25.9-2 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 libperl5.40_5.40.1-6 libperl5.42_5.42.0-2 libpipeline1_1.5.8-1 libproc2-0_2:4.0.4-9 libpsl5t64_0.21.2-1.1+b1 libpython3-stdlib_3.13.7-1 libpython3.13-minimal_3.13.9-1 libpython3.13-stdlib_3.13.9-1 libquadmath0_15.2.0-7 libreadline8t64_8.3-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2 libselinux1_3.9-2 libsemanage-common_3.9-1 libsemanage2_3.9-1 libsepol2_3.9-2 libsframe2_2.45-8 libsmartcols1_2.41.2-4 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python3-packaging_25.0-1 python3-yaml_6.0.2-2 python3.13_3.13.9-1 python3.13-minimal_3.13.9-1 readline-common_8.3-3 rpcsvc-proto_1.4.3-1 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 skesa_2.4.0-6+b2 spades_4.0.0+really3.15.5+dfsg-3 sqv_1.3.0-3 sysvinit-utils_3.15-5 tar_1.35+dfsg-3.1 tzdata_2025b-5 util-linux_2.41.2-4 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sun, 02 Nov 2025 17:03:39 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shovill Binary: shovill, shovill-examples Architecture: any all Version: 1.1.0-10 Maintainer: Debian Med Packaging Team Homepage: https://github.com/tseemann/shovill Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/shovill Vcs-Git: https://salsa.debian.org/med-team/shovill.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Build-Depends-Arch: spades, skesa, megahit Package-List: shovill deb science optional arch=any shovill-examples deb science optional arch=all Checksums-Sha1: ff674f771dd46d766ee38d7d019b019160412d52 6252102 shovill_1.1.0.orig.tar.gz 2b6a2e63adacceaccfe5d78ba9c5ebde154ff778 5692 shovill_1.1.0-10.debian.tar.xz Checksums-Sha256: b7323e6586238821202cf9644963e584e7397a5cee23e564d00b07fcb344ecd2 6252102 shovill_1.1.0.orig.tar.gz 5dd0c1dab3215e731bc7e0b2b27a06ce045962a8eb2479307ce3915a6a488f41 5692 shovill_1.1.0-10.debian.tar.xz Files: 1e988851741ece73311ff1fddb412172 6252102 shovill_1.1.0.orig.tar.gz fea482f432d78cf249196a0ecfbd3ea4 5692 shovill_1.1.0-10.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaQc/ABIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtor1AD9HDQZ744/wBxBpWLt5Opk+8cs4XrVhSy5 GEbPK3q6QVwBAK+0duubDnZxiFnNG6pRKrnpSpxmR36+JIEK5WylW/MP =luuC -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./shovill_1.1.0-10.dsc: no acceptable signature found dpkg-source: info: extracting shovill in /build/shovill-unbv12/shovill-1.1.0 dpkg-source: info: unpacking shovill_1.1.0.orig.tar.gz dpkg-source: info: unpacking shovill_1.1.0-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying adapter_commandline_arg.patch dpkg-source: info: applying fix-executable-names.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 02 Nov 2025 17:03:40 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network shovill_1.1.0-10 perl-5.42-throwaway amd64 ----------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network shovill_1.1.0-10 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/shovill-unbv12/shovill-1.1.0 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-31b28a97-5aab-478b-82ba-236715ea1170 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 shovill dpkg-buildpackage: info: source version 1.1.0-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building shovill using existing ./shovill_1.1.0.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building shovill in shovill_1.1.0-10.debian.tar.xz dpkg-source: info: building shovill in shovill_1.1.0-10.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shovill' in '../shovill_1.1.0-10_amd64.deb'. dpkg-deb: building package 'shovill-examples' in '../shovill-examples_1.1.0-10_all.deb'. dpkg-genbuildinfo -O../shovill_1.1.0-10_amd64.buildinfo dpkg-genchanges -O../shovill_1.1.0-10_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-11-02T17:03:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 02 Nov 2025 17:03:46 +0000 | +------------------------------------------------------------------------------+ shovill_1.1.0-10_amd64.changes: ------------------------------- Format: 1.8 Date: Sun, 02 Nov 2025 16:42:24 +0530 Source: shovill Binary: shovill shovill-examples Architecture: source all amd64 Version: 1.1.0-10 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: shovill - Assemble bacterial isolate genomes from Illumina paired-end reads shovill-examples - Test Data for shovill Changes: shovill (1.1.0-10) unstable; urgency=medium . * Team Upload. * Drop Redundant "Rules-Requires-Root: no" * Bump Standards-Version to 4.7.2 (no changes needed) * Drop fix-shebang.patch * Move d/watch to version 5 * Drop myself from uploaders Checksums-Sha1: e2156a488831b091a5024f2502b05b2bbabcdb43 1117 shovill_1.1.0-10.dsc 0e0a6aa6a62938b342838bd130b91eeb30152683 5696 shovill_1.1.0-10.debian.tar.xz 89b96861c8a5a40acbc0d4cbb7aa793102c850b8 6221020 shovill-examples_1.1.0-10_all.deb 62fd4847930555572cad9ac0febf52671b621a28 7235 shovill_1.1.0-10_amd64.buildinfo d75e29afeffdf4ec4adf65584824b5b07263f197 13612 shovill_1.1.0-10_amd64.deb Checksums-Sha256: 7a39a1bd1344d07c5cb14f9d030f130adea33c597a5bd2b254d0e1e597b14e1d 1117 shovill_1.1.0-10.dsc 44d8b1b619b65d7135dac9decdecf8c3bb667711c87aaf7b1f5a62c88a8ba029 5696 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shovill Binary: shovill shovill-examples Architecture: all amd64 source Version: 1.1.0-10 Checksums-Md5: 524009dc2d274c9d8d2b98d816a69595 1117 shovill_1.1.0-10.dsc 155154b453afe27bc96a948eababf3f6 6221020 shovill-examples_1.1.0-10_all.deb bab261c6501a57c797b8ac4d02158333 13612 shovill_1.1.0-10_amd64.deb Checksums-Sha1: e2156a488831b091a5024f2502b05b2bbabcdb43 1117 shovill_1.1.0-10.dsc 89b96861c8a5a40acbc0d4cbb7aa793102c850b8 6221020 shovill-examples_1.1.0-10_all.deb d75e29afeffdf4ec4adf65584824b5b07263f197 13612 shovill_1.1.0-10_amd64.deb Checksums-Sha256: 7a39a1bd1344d07c5cb14f9d030f130adea33c597a5bd2b254d0e1e597b14e1d 1117 shovill_1.1.0-10.dsc 15df201597dfa1777cd0f7edb8c0ab966c138348b892c3a1d7d3aa5b58c0c1ff 6221020 shovill-examples_1.1.0-10_all.deb 4bec5c045c8363ea908525191119aac4f365180557256004f7040a73770f6f84 13612 shovill_1.1.0-10_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 02 Nov 2025 17:03:46 +0000 Build-Path: /build/shovill-unbv12/shovill-1.1.0 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-2), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), bamtools (= 2.5.3+dfsg-1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.3-1), binutils (= 2.45-8), binutils-common (= 2.45-8), binutils-x86-64-linux-gnu (= 2.45-8), bsdextrautils (= 2.41.2-4), build-essential (= 12.12), bwa (= 0.7.19-1), 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 (= 15.2.0-7), cpp-15-x86-64-linux-gnu (= 15.2.0-7), cpp-x86-64-linux-gnu (= 4:15.2.0-4), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.28), debianutils (= 5.23.2), dh-autoreconf (= 21), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-4), g++-15 (= 15.2.0-7), g++-15-x86-64-linux-gnu (= 15.2.0-7), 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 (= 15.2.0-7), gcc-15-base (= 15.2.0-7), gcc-15-x86-64-linux-gnu (= 15.2.0-7), gcc-x86-64-linux-gnu (= 4:15.2.0-4), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.12-1), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-7), libatomic1 (= 15.2.0-7), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1), libbamtools2.5.3 (= 2.5.3+dfsg-1), libbinutils (= 2.45-8), libblkid1 (= 2.41.2-4), libboost-iostreams1.83.0 (= 1.83.0-5), libboost-program-options1.83.0 (= 1.83.0-5), libboost-timer1.83.0 (= 1.83.0-5), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-7), libcom-err2 (= 1.47.2-3+b3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-8), libctf0 (= 2.45-8), libcurl3t64-gnutls (= 8.17.0~rc3-1), libdb5.3t64 (= 5.3.28+dfsg2-10), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.28), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.3-1), libffi8 (= 3.5.2-2), libfile-stripnondeterminism-perl (= 1.15.0-1), libgcc-14-dev (= 14.3.0-10), libgcc-15-dev (= 15.2.0-7), libgcc-s1 (= 15.2.0-7), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgmp10 (= 2:6.3.0+dfsg-5), libgnutls30t64 (= 3.8.10-3), libgomp1 (= 15.2.0-7), libgprofng0 (= 2.45-8), libgssapi-krb5-2 (= 1.21.3-5), libhogweed6t64 (= 3.10.2-1), libhts3t64 (= 1.22.1+ds2-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 15.2.0-7), libidn2-0 (= 2.3.8-4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-7), libjansson4 (= 2.14-2+b3), libjsoncpp26 (= 1.9.6-4), libk5crypto3 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 15.2.0-7), liblzma5 (= 5.8.1-2), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmbedcrypto16 (= 3.6.4-2), libmbedtls21 (= 3.6.4-2), libmbedx509-7 (= 3.6.4-2), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.2-4), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libncbi-vdb3 (= 3.2.1+dfsg-2), libncurses6 (= 6.5+20250216-2), libncursesw6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.12.0-1), libngs-c++3 (= 3.2.1+dfsg-5), libngtcp2-16 (= 1.16.0-1), libngtcp2-crypto-gnutls8 (= 1.16.0-1), libnlopt0 (= 2.7.1-7), libp11-kit0 (= 0.25.9-2), 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 (= 5.42.0-2), libpipeline1 (= 1.5.8-1), libproc2-0 (= 2:4.0.4-9), libpsl5t64 (= 0.21.2-1.1+b1), libpython3-stdlib (= 3.13.7-1), libpython3.13-minimal (= 3.13.9-1), libpython3.13-stdlib (= 3.13.9-1), libquadmath0 (= 15.2.0-7), libreadline8t64 (= 8.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.9-2), libsframe2 (= 2.45-8), libsmartcols1 (= 2.41.2-4), libsqlite3-0 (= 3.46.1-8), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.5.4-1), libssw0 (= 1.1-15+b2), libstdc++-15-dev (= 15.2.0-7), libstdc++6 (= 15.2.0-7), libsystemd0 (= 258.1-2), libtasn1-6 (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-7), libtsan2 (= 15.2.0-7), libubsan1 (= 15.2.0-7), libuchardet0 (= 0.0.8-2), libudev1 (= 258.1-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.2-4), libxml2-16 (= 2.15.1+dfsg-0.3), libyaml-0-2 (= 0.2.5-2), libzstd1 (= 1.5.7+dfsg-2), linux-libc-dev (= 6.17.6-1), m4 (= 1.4.20-2), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), media-types (= 14.0.0), megahit (= 1.2.9-6), ncbi-vdb-data (= 3.2.1+dfsg-2), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), netbase (= 6.5), openssl-provider-legacy (= 3.5.4-1), patch (= 2.8-2), perl (= 5.42.0-2), perl-base (= 5.42.0-2), perl-modules-5.42 (= 5.42.0-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-9), python3 (= 3.13.7-1), python3-all (= 3.13.7-1), python3-joblib (= 1.4.2-5), python3-minimal (= 3.13.7-1), python3-packaging (= 25.0-1), python3-yaml (= 6.0.2-2), python3.13 (= 3.13.9-1), python3.13-minimal (= 3.13.9-1), readline-common (= 8.3-3), rpcsvc-proto (= 1.4.3-1), samtools (= 1.22.1-1), sed (= 4.9-2), sensible-utils (= 0.0.26), skesa (= 2.4.0-6+b2), spades (= 4.0.0+really3.15.5+dfsg-3), sysvinit-utils (= 3.15-5), tar (= 1.35+dfsg-3.1), tzdata (= 2025b-5), util-linux (= 2.41.2-4), xz-utils (= 5.8.1-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1762081944" +------------------------------------------------------------------------------+ | Package contents Sun, 02 Nov 2025 17:03:46 +0000 | +------------------------------------------------------------------------------+ shovill-examples_1.1.0-10_all.deb --------------------------------- new Debian package, version 2.0. size 6221020 bytes: control archive=968 bytes. 726 bytes, 21 lines control 618 bytes, 8 lines md5sums Package: shovill-examples Source: shovill Version: 1.1.0-10 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 6084 Section: science Priority: optional Multi-Arch: foreign Homepage: https://github.com/tseemann/shovill Description: Test Data for shovill Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. . This package contains a test data which can be used to test the package. drwxr-xr-x root/root 0 2025-11-02 11:12 ./ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/doc/shovill-examples/ -rw-r--r-- root/root 371 2025-11-02 11:12 ./usr/share/doc/shovill-examples/NEWS.Debian.gz -rw-r--r-- root/root 3081581 2025-11-02 11:12 ./usr/share/doc/shovill-examples/R1.fq.gz -rw-r--r-- root/root 3081822 2025-11-02 11:12 ./usr/share/doc/shovill-examples/R2.fq.gz -rw-r--r-- root/root 902 2025-11-02 11:12 ./usr/share/doc/shovill-examples/changelog.Debian.gz -rw-r--r-- root/root 866 2025-11-02 11:08 ./usr/share/doc/shovill-examples/copyright -rw-r--r-- root/root 52920 2020-03-13 05:35 ./usr/share/doc/shovill-examples/test.fna.gz -rw-r--r-- root/root 421 2020-03-13 05:35 ./usr/share/doc/shovill-examples/test.sh -rw-r--r-- root/root 1397 2020-03-13 05:35 ./usr/share/doc/shovill-examples/trimmomatic.fa shovill_1.1.0-10_amd64.deb -------------------------- new Debian package, version 2.0. size 13612 bytes: control archive=932 bytes. 775 bytes, 17 lines control 329 bytes, 5 lines md5sums Package: shovill Version: 1.1.0-10 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 40 Depends: perl:any, spades, velvet, skesa, megahit, flash, lighter, samtools, bwa, kmc, seqtk, pilon, trimmomatic, pigz, samclip Section: science Priority: optional Homepage: https://github.com/tseemann/shovill Description: Assemble bacterial isolate genomes from Illumina paired-end reads Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. drwxr-xr-x root/root 0 2025-11-02 11:12 ./ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/bin/ -rwxr-xr-x root/root 26613 2025-11-02 11:12 ./usr/bin/shovill drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/doc/shovill/ -rw-r--r-- root/root 371 2025-11-02 11:12 ./usr/share/doc/shovill/NEWS.Debian.gz -rw-r--r-- root/root 902 2025-11-02 11:12 ./usr/share/doc/shovill/changelog.Debian.gz -rw-r--r-- root/root 866 2025-11-02 11:08 ./usr/share/doc/shovill/copyright drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/man/ drwxr-xr-x root/root 0 2025-11-02 11:12 ./usr/share/man/man1/ -rw-r--r-- root/root 1062 2025-11-02 11:12 ./usr/share/man/man1/shovill.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 02 Nov 2025 17:03:46 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 02 Nov 2025 17:03:46 +0000 | +------------------------------------------------------------------------------+ Purging /build/shovill-unbv12 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 02 Nov 2025 17:03:47 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 18892 Build-Time: 6 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 10 Job: /srv/debomatic/incoming/shovill_1.1.0-10.dsc Machine Architecture: amd64 Package: shovill Package-Time: 21 Source-Version: 1.1.0-10 Space: 18892 Status: successful Version: 1.1.0-10 -------------------------------------------------------------------------------- Finished at 2025-11-02T17:03:46Z Build needed 00:00:21, 18892k disk space