sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | shovill 1.1.0-9 (amd64) Mon, 05 Aug 2024 01:21:06 +0000 | +==============================================================================+ Package: shovill Version: 1.1.0-9 Source Version: 1.1.0-9 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-2df91fdb-d68f-455e-a9df-cf89073ab1d6' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup shovill_1.1.0-9 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup shovill_1.1.0-9 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/shovill-QOHbfs/resolver-Eh3XMG' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 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 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/shovill_1.1.0-9.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/shovill-QOHbfs/shovill-1.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/shovill-QOHbfs' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, spades, skesa, megahit Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot, spades, skesa, megahit dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [660 B] Get:5 copy:/<>/apt_archive ./ Packages [673 B] Fetched 1942 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... The following additional packages will be installed: autoconf automake autopoint autotools-dev bamtools bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools2.5.2 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost-timer1.83.0 libbrotli1 libcom-err2 libcurl3t64-gnutls libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-c++3 libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libssh2-1t64 libssw0 libtool libuchardet0 libxml2 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-pkg-resources python3-yaml python3.12 python3.12-minimal samtools sensible-utils skesa spades tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools python3.12-venv python3.12-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-pytest python3-simplejson python3-psutil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bamtools bsdextrautils bwa debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools2.5.2 libboost-iostreams1.83.0 libboost-program-options1.83.0 libboost-timer1.83.0 libbrotli1 libcom-err2 libcurl3t64-gnutls libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncbi-vdb3 libncurses6 libnghttp2-14 libnghttp3-9 libngs-c++3 libngtcp2-16 libngtcp2-crypto-gnutls8 libnlopt0 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libssh2-1t64 libssw0 libtool libuchardet0 libxml2 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-pkg-resources python3-yaml python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy sensible-utils skesa spades tzdata 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. 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Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libnlopt0:amd64 (2.7.1-5+b4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Aug 5 01:21:17 UTC 2024. Universal Time is now: Mon Aug 5 01:21:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.35.1-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libboost-iostreams1.83.0:amd64 (1.83.0-3.1) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libproc2-0:amd64 (2:4.0.4-5) ... Setting up autopoint (0.22.5-2) ... Setting up libjsoncpp25:amd64 (1.9.5-6+b2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ... Setting up autoconf (2.71-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libngs-c++3:amd64 (3.0.3+dfsg-8) ... Setting up bamtools (2.5.2+dfsg-6) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libssw0:amd64 (1.1-15) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up libtool (2.4.7-7) ... Setting up python3.12 (3.12.4-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up groff-base (1.23.0-5) ... Setting up libpython3-stdlib:amd64 (3.12.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-1) ... Setting up python3 (3.12.4-1) ... /usr/share/spades/spades_pipeline/support.py:531: SyntaxWarning: invalid escape sequence '\d' return [atoi(c) for c in re.split("(\d+)", text)] Setting up skesa (2.4.0-6+b2) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (24.1-1) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-all (3.12.4-1) ... Setting up python3-yaml (6.0.1-2+b1) ... Setting up debhelper (13.16) ... Setting up samtools (1.20-3) ... Setting up megahit (1.2.9-5) ... Setting up spades (3.15.5+dfsg-7) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 bamtools_2.5.2+dfsg-6 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bwa_0.7.17-7+b3 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 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libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libcurl3t64-gnutls_8.9.1-1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdeflate0_1.20-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libexpat1_2.6.2-1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libjsoncpp25_1.9.5-6+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 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python3-all_3.12.4-1 python3-joblib_1.3.2-2 python3-minimal_3.12.4-1 python3-packaging_24.1-1 python3-pkg-resources_70.3.0-2 python3-yaml_6.0.1-2+b1 python3.12_3.12.4-3 python3.12-minimal_3.12.4-3 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 skesa_2.4.0-6+b2 spades_3.15.5+dfsg-7 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: shovill Binary: shovill, shovill-examples Architecture: any all Version: 1.1.0-9 Maintainer: Debian Med Packaging Team Uploaders: Nilesh Patra Homepage: https://github.com/tseemann/shovill Standards-Version: 4.6.1 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 010a7ff3692f58ee3d2b17a1261f3c2ed3cf949e 5768 shovill_1.1.0-9.debian.tar.xz Checksums-Sha256: b7323e6586238821202cf9644963e584e7397a5cee23e564d00b07fcb344ecd2 6252102 shovill_1.1.0.orig.tar.gz 4dcde0147b7ebabb22b827280fdbaad6a05bfaa3621012119280b28ccd8374c0 5768 shovill_1.1.0-9.debian.tar.xz Files: 1e988851741ece73311ff1fddb412172 6252102 shovill_1.1.0.orig.tar.gz f2ed89093cc36918d0b0c1eca690f42f 5768 shovill_1.1.0-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOChCgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEXhQ/+JX/XXakT5MVdkY6x6esXCZp8wfhJVNy9 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dpkg-source: info: extracting shovill in /<> dpkg-source: info: unpacking shovill_1.1.0.orig.tar.gz dpkg-source: info: unpacking shovill_1.1.0-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-shebang.patch 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 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network shovill_1.1.0-9 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network shovill_1.1.0-9 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-2df91fdb-d68f-455e-a9df-cf89073ab1d6 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package shovill dpkg-buildpackage: info: source version 1.1.0-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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_1.1.0-9.debian.tar.xz dpkg-source: info: building shovill in shovill_1.1.0-9.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_1.1.0-9_amd64.deb'. dpkg-deb: building package 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Tille Description: shovill - Assemble bacterial isolate genomes from Illumina paired-end reads shovill-examples - Test Data for shovill Changes: shovill (1.1.0-9) unstable; urgency=medium . * Team upload. * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: e70b06a0dad7b9955e3d2cf154a6167fca15de5a 1157 shovill_1.1.0-9.dsc c15c14a0891ec4de598e182c86183dd4ee803d5b 5776 shovill_1.1.0-9.debian.tar.xz a169b661add3a4c122b9c4b39d41b41c10cda4e2 6220876 shovill-examples_1.1.0-9_all.deb fffe5e9e687907e14b1bd861af98b1189c3fe198 7393 shovill_1.1.0-9_amd64.buildinfo 04d098f952dfdcf3a4702b11da7a04f468bda2d8 13488 shovill_1.1.0-9_amd64.deb Checksums-Sha256: 47a59456eea5a0a606dc3147f51f9d147816e0b0a21bf1255e13e5c94e02535e 1157 shovill_1.1.0-9.dsc 54bf625f5a3c7ef911ff69ca7c0c701a73d1c9abe209239e1de768bff79437ab 5776 shovill_1.1.0-9.debian.tar.xz 7ad6cb9855b730dffac2966b4ecff40d885bd158733f0df72e40bef6a25e03ad 6220876 shovill-examples_1.1.0-9_all.deb 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(= 2.5.2+dfsg-6), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bwa (= 0.7.17-7+b3), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbamtools2.5.2 (= 2.5.2+dfsg-6), libbinutils (= 2.42.90.20240720-2), libblkid1 (= 2.40.2-1), libboost-iostreams1.83.0 (= 1.83.0-3.1), libboost-program-options1.83.0 (= 1.83.0-3.1), libboost-timer1.83.0 (= 1.83.0-3.1), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-1), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libcurl3t64-gnutls (= 8.9.1-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdeflate0 (= 1.20-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexpat1 (= 2.6.2-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), libjsoncpp25 (= 1.9.5-6+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-2+b1), liblsan0 (= 14.2.0-1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmbedcrypto7t64 (= 2.28.8-1), libmbedtls14t64 (= 2.28.8-1), libmbedx509-1t64 (= 2.28.8-1), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncbi-vdb3 (= 3.0.2+dfsg-2+b1), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libngs-c++3 (= 3.0.3+dfsg-8), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libnlopt0 (= 2.7.1-5+b4), libp11-kit0 (= 0.25.5-2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libproc2-0 (= 2:4.0.4-5), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.12.4-1), libpython3.12-minimal (= 3.12.4-3), libpython3.12-stdlib (= 3.12.4-3), libquadmath0 (= 14.2.0-1), libreadline8t64 (= 8.2-4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libsqlite3-0 (= 3.46.0-1), libssh2-1t64 (= 1.11.0-7), libssl3t64 (= 3.3.1-2), libssw0 (= 1.1-15), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtasn1-6 (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libyaml-0-2 (= 0.2.5-1+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), media-types (= 10.1.0), megahit (= 1.2.9-5), ncbi-vdb-data (= 3.0.2+dfsg-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-5), python3 (= 3.12.4-1), python3-all (= 3.12.4-1), python3-joblib (= 1.3.2-2), python3-minimal (= 3.12.4-1), python3-packaging (= 24.1-1), python3-pkg-resources (= 70.3.0-2), python3-yaml (= 6.0.1-2+b1), python3.12 (= 3.12.4-3), python3.12-minimal (= 3.12.4-3), readline-common (= 8.2-4), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), skesa (= 2.4.0-6+b2), spades (= 3.15.5+dfsg-7), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1669497742" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ shovill-examples_1.1.0-9_all.deb -------------------------------- new Debian package, version 2.0. size 6220876 bytes: control archive=972 bytes. 725 bytes, 21 lines control 618 bytes, 8 lines md5sums Package: shovill-examples Source: shovill Version: 1.1.0-9 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 2022-11-26 21:22 ./ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/doc/shovill-examples/ -rw-r--r-- root/root 371 2022-11-26 21:22 ./usr/share/doc/shovill-examples/NEWS.Debian.gz -rw-r--r-- root/root 3081581 2022-11-26 21:22 ./usr/share/doc/shovill-examples/R1.fq.gz -rw-r--r-- root/root 3081822 2022-11-26 21:22 ./usr/share/doc/shovill-examples/R2.fq.gz -rw-r--r-- root/root 785 2022-11-26 21:22 ./usr/share/doc/shovill-examples/changelog.Debian.gz -rw-r--r-- root/root 866 2022-11-26 21:22 ./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_1.1.0-9_amd64.deb ------------------------- new Debian package, version 2.0. size 13488 bytes: control archive=932 bytes. 774 bytes, 17 lines control 329 bytes, 5 lines md5sums Package: shovill Version: 1.1.0-9 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 2022-11-26 21:22 ./ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/bin/ -rwxr-xr-x root/root 26612 2022-11-26 21:22 ./usr/bin/shovill drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/doc/shovill/ -rw-r--r-- root/root 371 2022-11-26 21:22 ./usr/share/doc/shovill/NEWS.Debian.gz -rw-r--r-- root/root 785 2022-11-26 21:22 ./usr/share/doc/shovill/changelog.Debian.gz -rw-r--r-- root/root 866 2022-11-26 21:22 ./usr/share/doc/shovill/copyright drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/man/ drwxr-xr-x root/root 0 2022-11-26 21:22 ./usr/share/man/man1/ -rw-r--r-- root/root 1062 2022-11-26 21:22 ./usr/share/man/man1/shovill.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 18932 Build-Time: 5 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 11 Job: /srv/debomatic/incoming/shovill_1.1.0-9.dsc Machine Architecture: amd64 Package: shovill Package-Time: 19 Source-Version: 1.1.0-9 Space: 18932 Status: successful Version: 1.1.0-9 -------------------------------------------------------------------------------- Finished at 2024-08-05T01:21:25Z Build needed 00:00:19, 18932k disk space