sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | shovill 1.1.0-9 (amd64) Mon, 16 Sep 2024 18:00:01 +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-6e1fc248-d23b-434f-ac5b-b190b454aca1' 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-9ETBks/resolver-Dw6elG' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://localhost:3142/debian sid InRelease Hit:3 http://deb.debian.org/debian unstable InRelease 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-9ETBks/shovill-1.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/shovill-9ETBks' 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 libnsl2 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libssh2-1t64 libssw0 libtirpc-common libtirpc3t64 libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types megahit ncbi-vdb-data netbase po-debconf procps python3 python3-all python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-typeguard python3-typing-extensions 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 libnsl2 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libssh2-1t64 libssw0 libtirpc-common libtirpc3t64 libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types megahit ncbi-vdb-data netbase po-debconf procps python3 python3-all python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-joblib python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-typeguard python3-typing-extensions python3-yaml python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy sensible-utils skesa spades tzdata 0 upgraded, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 45.5 MB of archives. After this operation, 182 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [896 B] Get:2 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:13 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get:21 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-5 [64.7 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-5 [878 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6 [159 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 bamtools amd64 2.5.2+dfsg-6 [206 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.18-1 [212 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:49 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83.0 amd64 1.83.0-3.2 [253 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3.2 [347 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2 [235 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.0-2 [359 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libngs-c++3 amd64 3.0.3+dfsg-9 [129 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libnlopt0 amd64 2.7.1-5+b4 [174 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libssw0 amd64 1.1-15 [20.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.5-1+b1 [1048 B] Get:85 http://deb.debian.org/debian unstable/main amd64 megahit amd64 1.2.9-5 [1163 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-1 [42.2 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:92 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 skesa amd64 2.4.0-6+b2 [571 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 spades amd64 3.15.5+dfsg-7 [9020 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.5 MB in 1s (38.0 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 22986 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 23306 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1+b1_amd64.deb ... Unpacking python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../15-libpython3-stdlib_3.12.5-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3-minimal (3.12.5-1+b1) ... Selecting previously unselected package python3. (Reading database ... 24348 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.5-1+b1_amd64.deb ... Unpacking python3 (3.12.5-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-5_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-5_amd64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-8_amd64.deb ... Unpacking bsdextrautils (2.40.2-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libbamtools2.5.2:amd64. Preparing to unpack .../18-libbamtools2.5.2_2.5.2+dfsg-6_amd64.deb ... Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../19-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... Selecting previously unselected package bamtools. Preparing to unpack .../20-bamtools_2.5.2+dfsg-6_amd64.deb ... Unpacking bamtools (2.5.2+dfsg-6) ... Selecting previously unselected package bwa. Preparing to unpack .../21-bwa_0.7.18-1_amd64.deb ... Unpacking bwa (0.7.18-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../22-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../23-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../24-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../25-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../26-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../27-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../28-libelf1t64_0.191-2_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../29-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../30-libicu72_72.1-5_amd64.deb ... Unpacking libicu72:amd64 (72.1-5) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../31-libxml2_2.12.7+dfsg-3+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-3+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../32-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../33-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../34-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../35-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libfakeroot:amd64. Preparing to unpack .../36-libfakeroot_1.36-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.36-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../37-fakeroot_1.36-1_amd64.deb ... Unpacking fakeroot (1.36-1) ... Selecting previously unselected package libboost-iostreams1.83.0:amd64. Preparing to unpack .../38-libboost-iostreams1.83.0_1.83.0-3.2_amd64.deb ... Unpacking libboost-iostreams1.83.0:amd64 (1.83.0-3.2) ... Selecting previously unselected package libboost-program-options1.83.0:amd64. Preparing to unpack .../39-libboost-program-options1.83.0_1.83.0-3.2_amd64.deb ... Unpacking libboost-program-options1.83.0:amd64 (1.83.0-3.2) ... Selecting previously unselected package libboost-timer1.83.0:amd64. Preparing to unpack .../40-libboost-timer1.83.0_1.83.0-3.2_amd64.deb ... Unpacking libboost-timer1.83.0:amd64 (1.83.0-3.2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../41-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../42-libnghttp2-14_1.63.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.63.0-1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../43-libnghttp3-9_1.4.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../44-libngtcp2-16_1.6.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../45-libngtcp2-crypto-gnutls8_1.6.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../46-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../47-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../48-libssh2-1t64_1.11.0-7_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../49-libcurl3t64-gnutls_8.10.0-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.10.0-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../50-libdeflate0_1.21-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.21-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../51-libhtscodecs2_1.6.1-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../52-libhts3t64_1.20+ds-1_amd64.deb ... Unpacking libhts3t64:amd64 (1.20+ds-1) ... Selecting previously unselected package libmbedcrypto7t64:amd64. Preparing to unpack .../53-libmbedcrypto7t64_2.28.8-1_amd64.deb ... Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedx509-1t64:amd64. Preparing to unpack .../54-libmbedx509-1t64_2.28.8-1_amd64.deb ... Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ... Selecting previously unselected package libmbedtls14t64:amd64. Preparing to unpack .../55-libmbedtls14t64_2.28.8-1_amd64.deb ... Unpacking libmbedtls14t64:amd64 (2.28.8-1) ... Selecting previously unselected package ncbi-vdb-data. Preparing to unpack .../56-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ... Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ... Selecting previously unselected package libncbi-vdb3:amd64. Preparing to unpack .../57-libncbi-vdb3_3.0.2+dfsg-2+b1_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../58-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package libngs-c++3:amd64. Preparing to unpack .../59-libngs-c++3_3.0.3+dfsg-9_amd64.deb ... Unpacking libngs-c++3:amd64 (3.0.3+dfsg-9) ... Selecting previously unselected package libnlopt0:amd64. Preparing to unpack .../60-libnlopt0_2.7.1-5+b4_amd64.deb ... Unpacking libnlopt0:amd64 (2.7.1-5+b4) ... Selecting previously unselected package libssw0:amd64. Preparing to unpack .../61-libssw0_1.1-15_amd64.deb ... Unpacking libssw0:amd64 (1.1-15) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../62-libyaml-0-2_0.2.5-1+b1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1+b1) ... Selecting previously unselected package python3-all. Preparing to unpack .../63-python3-all_3.12.5-1+b1_amd64.deb ... Unpacking python3-all (3.12.5-1+b1) ... Selecting previously unselected package megahit. Preparing to unpack .../64-megahit_1.2.9-5_amd64.deb ... Unpacking megahit (1.2.9-5) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../65-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../66-python3-more-itertools_10.4.0-1_all.deb ... Unpacking python3-more-itertools (10.4.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../67-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../68-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../69-python3-inflect_7.3.1-1_all.deb ... Unpacking python3-inflect (7.3.1-1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../70-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../71-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../72-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../73-python3-joblib_1.3.2-2_all.deb ... Unpacking python3-joblib (1.3.2-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../74-python3-packaging_24.1-1_all.deb ... Unpacking python3-packaging (24.1-1) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../75-python3-yaml_6.0.2-1_amd64.deb ... Unpacking python3-yaml (6.0.2-1) ... Selecting previously unselected package samtools. Preparing to unpack .../76-samtools_1.20-3_amd64.deb ... Unpacking samtools (1.20-3) ... Selecting previously unselected package skesa. Preparing to unpack .../77-skesa_2.4.0-6+b2_amd64.deb ... Unpacking skesa (2.4.0-6+b2) ... Selecting previously unselected package spades. Preparing to unpack .../78-spades_3.15.5+dfsg-7_amd64.deb ... Unpacking spades (3.15.5+dfsg-7) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../79-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-3.2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libboost-timer1.83.0:amd64 (1.83.0-3.2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up bwa (0.7.18-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... 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 (1.36-1) ... 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 Sep 16 18:00:14 UTC 2024. Universal Time is now: Mon Sep 16 18:00:14 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... 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 (1.83.0-3.2) ... 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 (2.72-3) ... 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-9) ... 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 libtool (2.4.7-7) ... 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 libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.0-2) ... Setting up skesa (2.4.0-6+b2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... /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 python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.5-1+b1) ... Setting up python3-yaml (6.0.2-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up megahit (1.2.9-5) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up spades (3.15.5+dfsg-7) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | 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_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-5 gcc-13_13.3.0-6 gcc-14_14.2.0-5 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 bamtools_2.5.2+dfsg-6 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bwa_0.7.18-1 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-5 cpp-14-x86-64-linux-gnu_14.2.0-5 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 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+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-5 g++-14-x86-64-linux-gnu_14.2.0-5 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-5 gcc-14-base_14.2.0-5 gcc-14-x86-64-linux-gnu_14.2.0-5 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 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 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-5 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-5 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbamtools2.5.2_2.5.2+dfsg-6 libbinutils_2.43.1-4 libblkid1_2.40.2-8 libboost-iostreams1.83.0_1.83.0-3.2 libboost-program-options1.83.0_1.83.0-3.2 libboost-timer1.83.0_1.83.0-3.2 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-5 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libcurl3t64-gnutls_8.10.0-2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate0_1.21-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libexpat1_2.6.3-1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-5 libgcc-s1_14.2.0-5 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-5 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-5 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.27-1 libitm1_14.2.0-5 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-3+b1 liblsan0_14.2.0-5 liblz4-1_1.9.4-3 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_2.40.2-8 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_1.63.0-1 libnghttp3-9_1.4.0-1 libngs-c++3_3.0.3+dfsg-9 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnlopt0_2.7.1-5+b4 libnpth0t64_1.6-3.1 libnsl2_1.3.0-3+b2 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 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-5 libpipeline1_1.5.8-1 libproc2-0_2:4.0.4-5 libpsl5t64_0.21.2-1.1 libpython3-stdlib_3.12.5-1+b1 libpython3.12-minimal_3.12.6-1 libpython3.12-stdlib_3.12.6-1 libquadmath0_14.2.0-5 libreadline8t64_8.2-5 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-4 libsmartcols1_2.40.2-8 libsqlite3-0_3.46.1-1 libssh2-1t64_1.11.0-7 libssl3t64_3.3.2-1 libssw0_1.1-15 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-5 libstdc++6_14.2.0-5 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtool_2.4.7-7 libtsan2_14.2.0-5 libubsan1_14.2.0-5 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 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 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 procps_2:4.0.4-5 python3_3.12.5-1+b1 python3-all_3.12.5-1+b1 python3-autocommand_2.2.2-3 python3-inflect_7.3.1-1 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.0.2-1 python3-joblib_1.3.2-2 python3-minimal_3.12.5-1+b1 python3-more-itertools_10.4.0-1 python3-packaging_24.1-1 python3-pkg-resources_74.1.2-2 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-yaml_6.0.2-1 python3.12_3.12.6-1 python3.12-minimal_3.12.6-1 readline-common_8.2-5 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_3.10-2 tar_1.35+dfsg-3 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-8 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 GXQuCru4pHdoZzEPEHEX23ELnHO+Q3z8D1pQ7MR5Y3Vw5gE4L58+jkA0P03TWv1Z oVJLHrX7X+XzxQ7I5ifwqnDUQVSQLqlwsmwOY0GoX+kUfKQgA624bzY9FMTztulD iv6Tv2I30M1fv7v0GxSZpEaf9Ipejrq8A+/jhpWNik4Cx+NcE+vJSbaH+/RWaJaZ /7EFqwdiI4+wtMOFf7RrUD2SeGmmV8DozLL+NZxAFoFO02FMHughBadXY4AVWTtV KmNupoPPCZ/uAUAIaGkjoEgS7VY1pOnD7sY8WxEOJDhwIK9K0E7QyrlF2ARAyHmZ wzACPQ9oHetbvDHwSkYDx8SNyAImKkQwv9WMwsYrdb6IjRM7+nwyeBllzMgWs/Dq JyimY5Jh6duTSGskuftmdCbZFerKGgMIoejpSC7T63Tol3gUbE1kbEzoMcoPwzDJ 3SD0X9T50sZrl1xMgbOh3gn5ZG7Khv47e38zuEf7iMUgWIl+gCceNTevex4daMWg xOieY3WNEDqXYmX6WbrVqjDCVmlohWvMhSSDsSURxr7vh2kwCCPxIb0DXW6NwC99 ZaPWqonkZIqi+qskmK/BtkplbwQv1gqzpdwpqP02QKXkzTolwOFkUE2fEf/JHcIq 6mfRYwFKLlE= =OzsJ -----END PGP SIGNATURE----- gpgv: Signature made Sat Nov 26 21:24:56 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shovill_1.1.0-9.dsc: no acceptable signature found 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-6e1fc248-d23b-434f-ac5b-b190b454aca1 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-examples' in '../shovill-examples_1.1.0-9_all.deb'. dpkg-deb: building package 'shovill' in '../shovill_1.1.0-9_amd64.deb'. dpkg-genbuildinfo -O../shovill_1.1.0-9_amd64.buildinfo dpkg-genchanges -O../shovill_1.1.0-9_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 2024-09-16T18:00:23Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ shovill_1.1.0-9_amd64.changes: ------------------------------ Format: 1.8 Date: Sat, 26 Nov 2022 22:22:22 +0100 Source: shovill Binary: shovill shovill-examples Architecture: source all amd64 Version: 1.1.0-9 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas 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 2862b9ad6ec6299971734876c63f99454bdbdee5 7683 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 aaf7593e7f560c3b8ceb1cc0db8da3179463eb29e737884d5b0cc3ff8282e3ce 7683 shovill_1.1.0-9_amd64.buildinfo f648c19fe514a541e6ca6495f3d99269fa504888757f8a07f2a6536133fea77c 13488 shovill_1.1.0-9_amd64.deb Files: bcd6c8d821b8fb81449b19d93ebbe961 1157 science optional shovill_1.1.0-9.dsc 3bfc42781ad88cf6c5de527413de7c20 5776 science optional shovill_1.1.0-9.debian.tar.xz e89340be766f7fea447e9be4c6e06b79 6220876 science optional shovill-examples_1.1.0-9_all.deb c6c95695a3c7653e721dece0aaeb9fd7 7683 science optional shovill_1.1.0-9_amd64.buildinfo 17ed6cadd0b6dd8fc411afb3b24ee02c 13488 science optional shovill_1.1.0-9_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: shovill Binary: shovill shovill-examples Architecture: all amd64 source Version: 1.1.0-9 Checksums-Md5: bcd6c8d821b8fb81449b19d93ebbe961 1157 shovill_1.1.0-9.dsc e89340be766f7fea447e9be4c6e06b79 6220876 shovill-examples_1.1.0-9_all.deb 17ed6cadd0b6dd8fc411afb3b24ee02c 13488 shovill_1.1.0-9_amd64.deb Checksums-Sha1: e70b06a0dad7b9955e3d2cf154a6167fca15de5a 1157 shovill_1.1.0-9.dsc a169b661add3a4c122b9c4b39d41b41c10cda4e2 6220876 shovill-examples_1.1.0-9_all.deb 04d098f952dfdcf3a4702b11da7a04f468bda2d8 13488 shovill_1.1.0-9_amd64.deb Checksums-Sha256: 47a59456eea5a0a606dc3147f51f9d147816e0b0a21bf1255e13e5c94e02535e 1157 shovill_1.1.0-9.dsc 7ad6cb9855b730dffac2966b4ecff40d885bd158733f0df72e40bef6a25e03ad 6220876 shovill-examples_1.1.0-9_all.deb f648c19fe514a541e6ca6495f3d99269fa504888757f8a07f2a6536133fea77c 13488 shovill_1.1.0-9_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 16 Sep 2024 18:00:22 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), bamtools (= 2.5.2+dfsg-6), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bwa (= 0.7.18-1), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-5), cpp-14-x86-64-linux-gnu (= 14.2.0-5), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), 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 (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-5), g++-14-x86-64-linux-gnu (= 14.2.0-5), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-5), gcc-14-base (= 14.2.0-5), gcc-14-x86-64-linux-gnu (= 14.2.0-5), 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 (= 14.2.0-5), libatomic1 (= 14.2.0-5), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbamtools2.5.2 (= 2.5.2+dfsg-6), libbinutils (= 2.43.1-4), libblkid1 (= 2.40.2-8), libboost-iostreams1.83.0 (= 1.83.0-3.2), libboost-program-options1.83.0 (= 1.83.0-3.2), libboost-timer1.83.0 (= 1.83.0-3.2), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-5), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libcurl3t64-gnutls (= 8.10.0-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate0 (= 1.21-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexpat1 (= 2.6.3-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-5), libgcc-s1 (= 14.2.0-5), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-5), libgprofng0 (= 2.43.1-4), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-5), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-5), 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-3+b1), liblsan0 (= 14.2.0-5), 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 (= 2.40.2-8), 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 (= 1.63.0-1), libnghttp3-9 (= 1.4.0-1), libngs-c++3 (= 3.0.3+dfsg-9), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libnlopt0 (= 2.7.1-5+b4), libnsl2 (= 1.3.0-3+b2), 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 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libproc2-0 (= 2:4.0.4-5), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-5), libreadline8t64 (= 8.2-5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.0-7), libssl3t64 (= 3.3.2-1), libssw0 (= 1.1-15), libstdc++-14-dev (= 14.2.0-5), libstdc++6 (= 14.2.0-5), libsystemd0 (= 256.6-1), libtasn1-6 (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-5), libubsan1 (= 14.2.0-5), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libxml2 (= 2.12.7+dfsg-3+b1), libyaml-0-2 (= 0.2.5-1+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), 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), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-5), python3 (= 3.12.5-1+b1), python3-all (= 3.12.5-1+b1), python3-autocommand (= 2.2.2-3), python3-inflect (= 7.3.1-1), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.0.2-1), python3-joblib (= 1.3.2-2), python3-minimal (= 3.12.5-1+b1), python3-more-itertools (= 10.4.0-1), python3-packaging (= 24.1-1), python3-pkg-resources (= 74.1.2-2), python3-typeguard (= 4.3.0-1), python3-typing-extensions (= 4.12.2-2), python3-yaml (= 6.0.2-1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), readline-common (= 8.2-5), 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 (= 3.10-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-8), 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: 12 Job: /srv/debomatic/incoming/shovill_1.1.0-9.dsc Machine Architecture: amd64 Package: shovill Package-Time: 22 Source-Version: 1.1.0-9 Space: 18932 Status: successful Version: 1.1.0-9 -------------------------------------------------------------------------------- Finished at 2024-09-16T18:00:23Z Build needed 00:00:22, 18932k disk space