https://launchpad.net/ubuntu/+source/iva/1.0.11+ds-3/+build/24893442 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-072 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 aarch64 Buildd toolchain package versions: launchpad-buildd_223~593~ubuntu20.04.1 python3-lpbuildd_223~593~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.6 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 2 Dec 23:22:23 ntpdate[1834]: adjust time server 10.211.37.1 offset 0.002308 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24893442 --image-type chroot /home/buildd/filecache-default/8c5cd40452e1382c60289b199b451f1850e898be Creating target for build PACKAGEBUILD-24893442 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24893442 Starting target for build PACKAGEBUILD-24893442 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24893442 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24893442 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24893442 Updating target for build PACKAGEBUILD-24893442 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main armhf Packages [1326 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe armhf Packages [13.5 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5845 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf Packages [274 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [109 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf Packages [1269 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [548 kB] Fetched 24.0 MB in 11s (2176 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: lsb-base* The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: adduser advancecomp apt binutils binutils-arm-linux-gnueabihf binutils-common bsdutils debconf debianutils e2fsprogs fakeroot gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libassuan0 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libext2fs2 libfakeroot libfdisk1 libffi8 libgpg-error0 libgssapi-krb5-2 libip4tc2 libjson-c5 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libmount1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libreadline8 libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libss2 libssl3 libuuid1 linux-libc-dev login logsave mount openssl passwd perl perl-base pinentry-curses readline-common sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 77 upgraded, 2 newly installed, 1 to remove and 0 not upgraded. Need to get 28.2 MB of archives. After this operation, 46.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf bsdutils armhf 1:2.38.1-4ubuntu1 [87.8 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf debianutils armhf 5.7-0.4 [102 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf grep armhf 3.8-3 [155 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main armhf login armhf 1:4.13+dfsg1-1ubuntu1 [197 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libperl5.36 armhf 5.36.0-4ubuntu2 [4043 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl armhf 5.36.0-4ubuntu2 [235 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf perl-base armhf 5.36.0-4ubuntu2 [1621 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcrypt-dev armhf 1:4.4.33-1 [120 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcrypt1 armhf 1:4.4.33-1 [91.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf zlib1g armhf 1:1.2.13.dfsg-1ubuntu2 [48.8 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main armhf tar armhf 1.34+dfsg-1.1 [269 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main armhf libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcap-ng0 armhf 0.8.3-1build1 [13.5 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main armhf libaudit1 armhf 1:3.0.7-1ubuntu2 [42.7 kB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libsmartcols1 armhf 2.38.1-4ubuntu1 [95.4 kB] Get:17 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf util-linux-extra armhf 2.38.1-4ubuntu1 [98.3 kB] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf util-linux armhf 2.38.1-4ubuntu1 [1159 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main armhf usrmerge all 33ubuntu1 [57.0 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf init-system-helpers all 1.65.2 [38.1 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf sysvinit-utils armhf 3.05-7ubuntu1 [25.9 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblz4-1 armhf 1.9.4-1 [57.6 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblzma5 armhf 5.2.8-0.0 [89.2 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libapt-pkg6.0 armhf 2.5.4 [911 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf debconf all 1.5.80 [125 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main armhf libpam0g armhf 1.5.2-5ubuntu1 [54.9 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main armhf libselinux1 armhf 3.4-1build1 [69.3 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main armhf libpam-modules-bin armhf 1.5.2-5ubuntu1 [41.1 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main armhf libpam-modules armhf 1.5.2-5ubuntu1 [266 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main armhf passwd armhf 1:4.13+dfsg1-1ubuntu1 [814 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf adduser all 3.129ubuntu1 [59.0 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libgpg-error0 armhf 1.46-1 [60.4 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main armhf gpgv armhf 2.2.40-1ubuntu1 [193 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main armhf libseccomp2 armhf 2.5.4-1ubuntu2 [45.9 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf apt armhf 2.5.4 [1371 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf logsave armhf 1.46.6~rc1-1ubuntu1 [9960 B] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libext2fs2 armhf 1.46.6~rc1-1ubuntu1 [188 kB] Get:38 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf e2fsprogs armhf 1.46.6~rc1-1ubuntu1 [564 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf mount armhf 2.38.1-4ubuntu1 [125 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf init armhf 1.65.2 [4810 B] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libblkid1 armhf 2.38.1-4ubuntu1 [137 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libmount1 armhf 2.38.1-4ubuntu1 [152 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main armhf libpam-runtime all 1.5.2-5ubuntu1 [40.0 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libuuid1 armhf 2.38.1-4ubuntu1 [23.8 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libffi8 armhf 3.4.4-1 [20.2 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcom-err2 armhf 1.46.6~rc1-1ubuntu1 [8860 B] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libss2 armhf 1.46.6~rc1-1ubuntu1 [10.1 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libapparmor1 armhf 3.0.7-1ubuntu4 [32.3 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libjson-c5 armhf 0.16-2 [29.0 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libssl3 armhf 3.0.5-2ubuntu2 [1560 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libcryptsetup12 armhf 2:2.5.0-6ubuntu2 [196 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libfdisk1 armhf 2.38.1-4ubuntu1 [186 kB] Get:53 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-1 [118 kB] Get:54 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libkrb5-3 armhf 1.20.1-1 [321 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libkrb5support0 armhf 1.20.1-1 [29.6 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libk5crypto3 armhf 1.20.1-1 [78.4 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libip4tc2 armhf 1.8.7-1ubuntu7 [17.4 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf readline-common all 8.2-1.2 [55.2 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libreadline8 armhf 8.2-1.2 [128 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libsqlite3-0 armhf 3.40.0-1 [563 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf openssl armhf 3.0.5-2ubuntu2 [1148 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main armhf tzdata all 2022g-0ubuntu2 [401 kB] Get:63 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libpng16-16 armhf 1.6.39-2 [166 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf xz-utils armhf 5.2.8-0.0 [142 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main armhf advancecomp armhf 2.4-1 [190 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libctf-nobfd0 armhf 2.39-8ubuntu2 [85.4 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libctf0 armhf 2.39-8ubuntu2 [85.9 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.39-8ubuntu2 [2764 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libbinutils armhf 2.39-8ubuntu2 [438 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils armhf 2.39-8ubuntu2 [3106 B] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf binutils-common armhf 2.39-8ubuntu2 [223 kB] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libfakeroot armhf 1.30.1-1ubuntu1 [26.4 kB] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf fakeroot armhf 1.30.1-1ubuntu1 [61.6 kB] Get:74 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libassuan0 armhf 2.5.5-5 [30.6 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main armhf pinentry-curses armhf 1.2.1-1ubuntu1 [35.8 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main armhf gpg armhf 2.2.40-1ubuntu1 [482 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main armhf gpgconf armhf 2.2.40-1ubuntu1 [117 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main armhf gpg-agent armhf 2.2.40-1ubuntu1 [236 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf linux-libc-dev armhf 5.19.0-23.24 [1306 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.2 MB in 2s (11.6 MB/s) (Reading database ... 13288 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24893442 armhf lunar-proposed -c chroot:build-PACKAGEBUILD-24893442 --arch=armhf --dist=lunar-proposed --nolog iva_1.0.11+ds-3.dsc Initiating build PACKAGEBUILD-24893442 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-072.buildd +==============================================================================+ | iva 1.0.11+ds-3 (armhf) Fri, 02 Dec 2022 23:23:27 +0000 | +==============================================================================+ Package: iva Version: 1.0.11+ds-3 Source Version: 1.0.11+ds-3 Distribution: lunar-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24893442/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/iva-GifaZ4/resolver-IBKJf1' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iva_1.0.11+ds-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/iva-GifaZ4/iva-1.0.11+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-GifaZ4' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq, kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq, kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless, build-essential, fakeroot 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 [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [481 B] Get:5 copy:/<>/apt_archive ./ Packages [563 B] Fetched 2001 B in 0s (36.6 kB/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 packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdw1 libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libicu71 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2 m4 man-db media-types mummer openjdk-17-jdk-headless openjdk-17-jre-headless po-debconf python3 python3-attr python3-decorator python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pysam python3-pytest python3-setuptools python3-tomli python3.10 python3.10-minimal python3.11 python3.11-minimal samtools smalt ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make default-jre flit python3-build python3-installer gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl cups-common low-memory-monitor liblcms2-utils pcscd libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-17-demo openjdk-17-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc python-networkx-doc python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy gfortran python-numpy-doc python3-dev subversion python-pyparsing-doc python-setuptools-doc python3.10-venv python3.10-doc binfmt-support python3.11-venv python3.11-doc cwltool Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl alsa-ucm-conf alsa-topology-conf bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-yaml python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdw1 libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libicu71 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2 m4 man-db media-types mummer openjdk-17-jdk-headless openjdk-17-jre-headless po-debconf python3 python3-attr python3-decorator python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pyparsing python3-pysam python3-pytest python3-setuptools python3-tomli python3.10 python3.10-minimal python3.11 python3.11-minimal samtools sbuild-build-depends-main-dummy smalt ucf 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. 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lunar/main armhf libicu71 armhf 71.1-3ubuntu1 [10.3 MB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.1 [588 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf python3-pkg-resources all 65.5.0-1 [208 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main armhf ucf all 3.0043 [56.1 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf bsdextrautils armhf 2.38.1-4ubuntu1 [76.4 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main armhf libmagic-mgc armhf 1:5.41-4 [257 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main armhf libmagic1 armhf 1:5.41-4 [80.1 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main armhf file armhf 1:5.41-4 [20.6 kB] Get:28 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gettext-base armhf 0.21-10 [37.3 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main armhf libuchardet0 armhf 0.0.7-1build2 [75.7 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main armhf groff-base armhf 1.22.4-9 [849 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main armhf libnghttp2-14 armhf 1.50.0-1 [68.2 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main armhf libpipeline1 armhf 1.5.7-1 [26.2 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main armhf libpsl5 armhf 0.21.0-1.2build2 [56.9 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main armhf man-db armhf 2.11.1-1 [1183 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main armhf m4 armhf 1.4.19-1 [236 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main armhf autoconf all 2.71-2 [338 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main armhf autotools-dev all 20220109.1 [44.9 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main armhf automake all 1:1.16.5-1.3 [558 kB] Get:39 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf autopoint all 0.21-10 [421 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main armhf libio-string-perl all 1.08-3.1 [10.7 kB] Get:41 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0.69-1 [16.0 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/universe armhf libsub-uplevel-perl all 0.2800-3 [11.6 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/universe armhf libtest-exception-perl all 0.43-3 [13.4 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/universe armhf libtest-warn-perl all 0.37-2 [12.6 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/universe armhf libtest-most-perl all 0.38-1 [21.5 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/universe armhf bioperl all 1.7.8-1 [216 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main armhf ca-certificates-java all 20220719 [12.4 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libtool all 2.4.7-5 [166 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main armhf dh-autoreconf all 20 [16.1 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main armhf libsub-override-perl all 0.09-4 [8706 B] Get:62 http://ftpmaster.internal/ubuntu lunar/main armhf libfile-stripnondeterminism-perl all 1.13.0-2 [18.2 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main armhf dh-strip-nondeterminism all 1.13.0-2 [5308 B] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libdw1 armhf 0.188-1 [224 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main armhf debugedit armhf 1:5.0-5 [42.8 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main armhf dwz armhf 0.14+20220924-2 [109 kB] Get:67 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf gettext armhf 0.21-10 [802 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf debhelper all 13.10.1ubuntu1 [924 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kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main armhf fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main armhf fontconfig-config all 2.13.1-4.4ubuntu1 [28.2 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main armhf libfontconfig1 armhf 2.13.1-4.4ubuntu1 [107 kB] Get:84 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libnspr4 armhf 2:4.35-1 [92.8 kB] Get:85 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libnss3 armhf 2:3.85-1 [1226 kB] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libasound2-data all 1.2.8-1 [19.4 kB] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libasound2 armhf 1.2.8-1 [342 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main armhf libgraphite2-3 armhf 1.3.14-1build2 [65.2 kB] Get:89 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libharfbuzz0b armhf 5.2.0-2 [381 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main armhf libpcsclite1 armhf 1.9.9-1 [19.7 kB] Get:91 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf openjdk-17-jre-headless armhf 17.0.5+8-2ubuntu1 [42.1 MB] Get:92 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf default-jre-headless armhf 2:1.17-73 [2778 B] Get:93 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf openjdk-17-jdk-headless armhf 17.0.5+8-2ubuntu1 [176 MB] Get:94 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf default-jdk-headless armhf 2:1.17-73 [952 B] Get:95 http://ftpmaster.internal/ubuntu lunar/main armhf python3-lib2to3 all 3.10.8-1 [77.5 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main armhf python3-distutils all 3.10.8-1 [139 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/universe armhf dh-python all 5.20221122 [106 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-6ubuntu2 [18.7 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/main armhf libsasl2-2 armhf 2.1.28+dfsg-6ubuntu2 [52.4 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-1ubuntu1 [160 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build4 [52.8 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main armhf libssh-4 armhf 0.10.4-2 [163 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main armhf libcurl3-gnutls armhf 7.86.0-2 [247 kB] Get:104 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libdeflate0 armhf 1.14-1 [55.9 kB] Get:105 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf libhtscodecs2 armhf 1.3.0-4 [65.1 kB] Get:106 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf libhts3 armhf 1.16+ds-3 [372 kB] Get:107 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf samtools armhf 1.16.1-1 [562 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/universe armhf fastaq all 3.17.0-5 [47.9 kB] Get:109 http://ftpmaster.internal/ubuntu lunar/universe armhf help2man armhf 1.49.2 [196 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/universe armhf kmc armhf 3.2.1+dfsg-1 [1016 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/universe armhf libbambamc0 armhf 0.0.50-6 [33.7 kB] Get:112 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libblas3 armhf 3.11.0-2 [119 kB] Get:113 http://ftpmaster.internal/ubuntu lunar/main armhf libgfortran5 armhf 12.2.0-9ubuntu1 [295 kB] Get:114 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf liblapack3 armhf 3.11.0-2 [1994 kB] Get:115 http://ftpmaster.internal/ubuntu lunar/main armhf libpython3.11-stdlib armhf 3.11.0-3 [1735 kB] Get:116 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf libssl-dev armhf 3.0.5-2ubuntu2 [2075 kB] Get:117 http://ftpmaster.internal/ubuntu lunar/universe armhf mummer armhf 3.23+dfsg-7 [626 kB] Get:118 http://ftpmaster.internal/ubuntu lunar/main armhf python3-attr all 22.1.0-1 [48.5 kB] Get:119 http://ftpmaster.internal/ubuntu lunar/main armhf python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:120 http://ftpmaster.internal/ubuntu lunar/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] Get:121 http://ftpmaster.internal/ubuntu lunar/main armhf python3-more-itertools all 8.10.0-2 [47.9 kB] Get:122 http://ftpmaster.internal/ubuntu lunar/main armhf python3-networkx all 2.4-4ubuntu2 [872 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main armhf python3.11 armhf 3.11.0-3 [553 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main armhf python3-numpy armhf 1:1.21.5-1ubuntu1 [4846 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main armhf python3-pyparsing all 3.0.7-3 [82.1 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/main armhf python3-packaging all 21.3-1.1 [30.6 kB] Get:127 http://ftpmaster.internal/ubuntu lunar/universe armhf python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/universe armhf python3-py all 1.11.0-1 [73.2 kB] Get:129 http://ftpmaster.internal/ubuntu lunar-proposed/universe armhf python3-pysam armhf 0.20.0+ds-1 [1672 kB] Get:130 http://ftpmaster.internal/ubuntu lunar/universe armhf python3-tomli all 2.0.1-1 [16.6 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/universe armhf python3-pytest all 7.1.2-2ubuntu1 [219 kB] Get:132 http://ftpmaster.internal/ubuntu lunar-proposed/main armhf python3-setuptools all 65.5.0-1 [451 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/universe armhf smalt armhf 0.7.6-12 [107 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 273 MB in 14s (20.1 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15242 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4build4_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-4build4) ... Selecting previously unselected package libpython3.10-minimal:armhf. Preparing to unpack .../libpython3.10-minimal_3.10.8-3_armhf.deb ... Unpacking libpython3.10-minimal:armhf (3.10.8-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.8-3_armhf.deb ... Unpacking python3.10-minimal (3.10.8-3) ... Setting up libpython3.10-minimal:armhf (3.10.8-3) ... Setting up libexpat1:armhf (2.5.0-1) ... Setting up python3.10-minimal (3.10.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15559 files and directories currently installed.) 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Setting up libtest-deep-perl (1.130-2) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up gawk (1:5.1.0-1build3) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.74.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.10.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build7) ... Setting up libnghttp2-14:armhf (1.50.0-1) ... Setting up libmagic1:armhf (1:5.41-4) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-10) ... Setting up m4 (1.4.19-1) ... Setting up file (1:5.41-4) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-6ubuntu2) ... Setting up libasound2-data (1.2.8-1) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfreetype6:armhf (2.12.1+dfsg-3) ... Setting up libnspr4:armhf (2:4.35-1) ... Setting up libtext-diff-perl (1.45-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libavahi-common-data:armhf (0.8-6ubuntu1) ... Setting up libdbus-1-3:armhf (1.14.0-2ubuntu3) ... Setting up libbambamc0:armhf (0.0.50-6) ... Setting up libssl-dev:armhf (3.0.5-2ubuntu2) ... Setting up autopoint (0.21-10) ... Setting up fonts-dejavu-core (2.37-2build1) ... Setting up libpcsclite1:armhf (1.9.9-1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:armhf (2.1.2-0ubuntu1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-6ubuntu2) ... Setting up libssh-4:armhf (0.10.4-2) ... Setting up libgfortran5:armhf (12.2.0-9ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libuchardet0:armhf (0.0.7-1build2) ... Setting up libasound2:armhf (1.2.8-1) ... Setting up libmpdec3:armhf (2.5.1-2build2) ... Setting up mummer (3.23+dfsg-7) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:armhf (5.2.0-2) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libpython3.11-minimal:armhf (3.11.0-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up ca-certificates-java (20220719) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:EC-ACC.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem done. Setting up libelf1:armhf (0.188-1) ... Setting up kmc (3.2.1+dfsg-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.1) ... Setting up liblocale-gettext-perl (1.07-4build4) ... Setting up libjpeg8:armhf (8c-2ubuntu10) ... 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 (1.13.0-2) ... Setting up python3.11-minimal (3.11.0-3) ... Setting up smalt (0.7.6-12) ... Setting up libdw1:armhf (0.188-1) ... Setting up liblapack3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-10) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.13.1-4.4ubuntu1) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libpython3.11-stdlib:armhf (3.11.0-3) ... Setting up libavahi-common3:armhf (0.8-6ubuntu1) ... Setting up libtest-differences-perl (0.69-1) ... Setting up libnss3:armhf (2:3.85-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.2) ... Setting up libpython3.10-stdlib:armhf (3.10.8-3) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up dh-strip-nondeterminism (1.13.0-2) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up debugedit (1:5.0-5) ... Setting up libfontconfig1:armhf (2.13.1-4.4ubuntu1) ... Setting up libavahi-client3:armhf (0.8-6ubuntu1) ... Setting up libpython3-stdlib:armhf (3.10.6-1ubuntu1) ... Setting up python3.11 (3.11.0-3) ... Setting up python3.10 (3.10.8-3) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.86.0-2) ... Setting up python3 (3.10.6-1ubuntu1) ... Setting up man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (3.0.7-3) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up libcups2:armhf (2.4.2-1ubuntu2) ... Setting up python3-lib2to3 (3.10.8-1) ... Setting up python3-pkg-resources (65.5.0-1) ... Setting up python3-distutils (3.10.8-1) ... Setting up dh-python (5.20221122) ... Setting up bioperl (1.7.8-1) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.1.0-1) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up python3-pysam (0.20.0+ds-1) ... Setting up python3-setuptools (65.5.0-1) ... Setting up python3-tomli (2.0.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up python3-networkx (2.4-4ubuntu2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:933: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.nodes['n1']['special'] is 0 /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_graphml.py:935: SyntaxWarning: "is" with a literal. Did you mean "=="? assert H.edges['n0','n1',1]['special'] is 0 Setting up samtools (1.16.1-1) ... Setting up python3-packaging (21.3-1.1) ... Setting up python3-numpy (1:1.21.5-1ubuntu1) ... Setting up openjdk-17-jre-headless:armhf (17.0.5+8-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up default-jre-headless (2:1.17-73) ... Setting up python3-pytest (7.1.2-2ubuntu1) ... Setting up fastaq (3.17.0-5) ... Setting up openjdk-17-jdk-headless:armhf (17.0.5+8-2ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jdk-headless (2:1.17-73) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (251.4-1ubuntu7) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-135-generic #152-Ubuntu SMP Wed Nov 23 20:19:17 UTC 2022 arm64 (armv7l) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-12_12.2.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.129ubuntu1 advancecomp_2.4-1 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39-8ubuntu2 binutils-arm-linux-gnueabihf_2.39-8ubuntu2 binutils-common_2.39-8ubuntu2 bioperl_1.7.8-1 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 ca-certificates-java_20220719 coreutils_8.32-4.1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-9ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.80 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 default-jdk-headless_2:1.17-73 default-jre-headless_2:1.17-73 dh-autoreconf_20 dh-python_5.20221122 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-1 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1ubuntu1 fakeroot_1.30.1-1ubuntu1 fastaq_3.17.0-5 file_1:5.41-4 findutils_4.9.0-3ubuntu1 fontconfig-config_2.13.1-4.4ubuntu1 fonts-dejavu-core_2.37-2build1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-9ubuntu1 gawk_1:5.1.0-1build3 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-9ubuntu1 gcc-12-base_12.2.0-9ubuntu1 gettext_0.21-10 gettext-base_0.21-10 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 help2man_1.49.2 hostname_3.23ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 java-common_0.73 kmc_3.2.1+dfsg-1 libacl1_2.3.1-1 libalgorithm-diff-perl_1.201-1 libapparmor1_3.0.7-1ubuntu4 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-9ubuntu1 libasound2_1.2.8-1 libasound2-data_1.2.8-1 libassuan0_2.5.5-5 libatomic1_12.2.0-9ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1ubuntu2 libaudit1_1:3.0.7-1ubuntu2 libavahi-client3_0.8-6ubuntu1 libavahi-common-data_0.8-6ubuntu1 libavahi-common3_0.8-6ubuntu1 libbambamc0_0.0.50-6 libbinutils_2.39-8ubuntu2 libbio-perl-perl_1.7.8-1 libblas3_3.11.0-2 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build7 libbz2-1.0_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcap-ng0_0.8.3-1build1 libcap2_1:2.44-1build3 libcapture-tiny-perl_0.48-1 libcc1-0_12.2.0-9ubuntu1 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.46.6~rc1-1ubuntu1 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcryptsetup12_2:2.5.0-6ubuntu2 libctf-nobfd0_2.39-8ubuntu2 libctf0_2.39-8ubuntu2 libcups2_2.4.2-1ubuntu2 libcurl3-gnutls_7.86.0-2 libdata-stag-perl_0.14-3 libdb5.3_5.3.28+dfsg1-0.10 libdbus-1-3_1.14.0-2ubuntu3 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdeflate0_1.14-1 libdevel-stacktrace-perl_2.0400-2 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.9ubuntu1 libdw1_0.188-1 libelf1_0.188-1 libexception-class-perl_1.45-1 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1ubuntu1 libfakeroot_1.30.1-1ubuntu1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-2 libfontconfig1_2.13.1-4.4ubuntu1 libfreetype6_2.12.1+dfsg-3 libgcc-12-dev_12.2.0-9ubuntu1 libgcc-s1_12.2.0-9ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-9ubuntu1 libglib2.0-0_2.74.2-1 libgmp10_2:6.2.1+dfsg1-1ubuntu2 libgnutls30_3.7.7-2ubuntu2 libgomp1_12.2.0-9ubuntu1 libgpg-error0_1.46-1 libgraphite2-3_1.3.14-1build2 libgssapi-krb5-2_1.20.1-1 libharfbuzz0b_5.2.0-2 libhogweed6_3.8.1-2 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libio-string-perl_1.08-3.1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjson-c5_0.16-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkmod2_30+20220630-3ubuntu1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblapack3_3.11.0-2 liblcms2-2_2.13.1-1 libldap-2.5-0_2.5.13+dfsg-1ubuntu1 liblocale-gettext-perl_1.07-4build4 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma5_5.2.8-0.0 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-4ubuntu1 libmpc3_1.2.1-2build1 libmpdec3_2.5.1-2build2 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libnspr4_2:4.35-1 libnss3_2:3.85-1 libp11-kit0_0.24.1-1ubuntu2 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpcre2-8-0_10.40-1ubuntu1 libpcre3_2:8.39-14 libpcsclite1_1.9.9-1 libperl5.34_5.34.0-5ubuntu1 libperl5.36_5.36.0-4ubuntu2 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.0-1.2build2 libpython3-stdlib_3.10.6-1ubuntu1 libpython3.10-minimal_3.10.8-3 libpython3.10-stdlib_3.10.8-3 libpython3.11-minimal_3.11.0-3 libpython3.11-stdlib_3.11.0-3 libreadline8_8.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg-6ubuntu2 libsasl2-modules-db_2.1.28+dfsg-6ubuntu2 libseccomp2_2.5.4-1ubuntu2 libselinux1_3.4-1build1 libsemanage-common_3.4-1build1 libsemanage2_3.4-1build1 libsepol2_3.4-2 libsigsegv2_2.14-1ubuntu1 libsmartcols1_2.38.1-4ubuntu1 libsqlite3-0_3.40.0-1 libss2_1.46.6~rc1-1ubuntu1 libssh-4_0.10.4-2 libssl-dev_3.0.5-2ubuntu2 libssl3_3.0.5-2ubuntu2 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 libsub-override-perl_0.09-4 libsub-uplevel-perl_0.2800-3 libsystemd-shared_251.4-1ubuntu7 libsystemd0_251.4-1ubuntu7 libtasn1-6_4.19.0-2 libtest-deep-perl_1.130-2 libtest-differences-perl_0.69-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-diff-perl_1.45-1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libubsan1_12.2.0-9ubuntu1 libuchardet0_0.0.7-1build2 libudev1_251.4-1ubuntu7 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libxml2_2.9.14+dfsg-1.1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.0-23.24 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.46.6~rc1-1ubuntu1 lto-disabled-list_36 m4_1.4.19-1 make_4.3-4.1build1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-4ubuntu1 mummer_3.23+dfsg-7 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openjdk-17-jdk-headless_17.0.5+8-2ubuntu1 openjdk-17-jre-headless_17.0.5+8-2ubuntu1 openssl_3.0.5-2ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-4ubuntu2 perl-base_5.36.0-4ubuntu2 perl-modules-5.34_5.34.0-5ubuntu1 perl-modules-5.36_5.36.0-4ubuntu2 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-7ubuntu1 python3_3.10.6-1ubuntu1 python3-attr_22.1.0-1 python3-decorator_4.4.2-0ubuntu1 python3-distutils_3.10.8-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1ubuntu1 python3-more-itertools_8.10.0-2 python3-networkx_2.4-4ubuntu2 python3-numpy_1:1.21.5-1ubuntu1 python3-packaging_21.3-1.1 python3-pkg-resources_65.5.0-1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pyparsing_3.0.7-3 python3-pysam_0.20.0+ds-1 python3-pytest_7.1.2-2ubuntu1 python3-setuptools_65.5.0-1 python3-tomli_2.0.1-1 python3.10_3.10.8-3 python3.10-minimal_3.10.8-3 python3.11_3.11.0-3 python3.11-minimal_3.11.0-3 readline-common_8.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 smalt_0.7.6-12 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.05-7ubuntu1 tar_1.34+dfsg-1.1 tzdata_2022g-0ubuntu2 ubuntu-keyring_2021.03.26 ucf_3.0043 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 xz-utils_5.2.8-0.0 zlib1g_1:1.2.13.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.11+ds-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Testsuite: autopkgtest Testsuite-Triggers: python3-packaging, trimmomatic Build-Depends: debhelper-compat (= 13), dh-python, libssl-dev, bioperl, fastaq, kmc (>= 3.1), help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless Package-List: iva deb science optional arch=any Checksums-Sha1: f333165445174c86c83460fe990b625f7ae3aff5 8680588 iva_1.0.11+ds.orig.tar.xz 928ed4c3923ed82a9a9657bd5991cabdf95bb9a1 5940 iva_1.0.11+ds-3.debian.tar.xz Checksums-Sha256: 0835a11746deaa4067aeb1bc9817ed8d415f36de51ae4fc122ea5b287c5ecf1d 8680588 iva_1.0.11+ds.orig.tar.xz 72b271624ad0750a915c0a08a6c566291778e7511540677bbffefb5da206ff01 5940 iva_1.0.11+ds-3.debian.tar.xz Files: e7b6c8d9cc2adb23b0d90168122c33b3 8680588 iva_1.0.11+ds.orig.tar.xz 468b8d0b60b08e1e0c6cc2374f5f26d1 5940 iva_1.0.11+ds-3.debian.tar.xz Dgit: e695f282106cdbcb785cfec0de19cc289b6e25bd debian archive/debian/1.0.11+ds-3 https://git.dgit.debian.org/iva -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOKMhMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoGwg/9EFvVJz/x63B5ifdFJXCT2Ga8l+ZW OctWF8dDrG+lt4hvhah+TUG3LPPxgltgUBYRH3+IHMin4o+S5Up5oFjN5MUlte3n 5roHq8qgtwoD0A3TGI+DZ7uwFreKYFA3CuEoREpmYILpJg1FZwjXvsujzzZHQS3c t9cCXUWRnTI1H9aBNQYaKdgk/9fqzGpbeYpqPNFAFwrGTQoxqbcNiiP2SERGMN0t /ysYat+UOalxVrougqKBbf3UIjc8hnhMohFPHWAxJnmXWmxG7c5NUeHLUR8RqwW/ otkTS5uewvPtSB+JwFxNLQva/wEMBlwJF/aDrAYrn91zzWGSkCdyrH9wt7iDos1+ +4hgRVxLmY4AZsrWweQdrGDsQxkq5YOUyd04dzhI1iY3h/GsUcvTXT3OzPDiodtP JNHAFetQ7gAwBS33fRHCWh7mgTzvfnSpSG0yyoKw/cdmZn90rrePrDGLtSQqRZPn fTi4zI7EfOVQ/SGOdcLDmKNVtqurQO7Z1req+VNLLBZVIQtPL2OKUvWvb2ZNnKGD tG+wqtj4Y/EOjxcGvBWVRe0C3sYa17SppV8G9sVXNgpZuKbM+IShf+r+XmKMRvGt dMm0S9Aq+4NGg0+4mVYItrphUgI+GAcmngiFUTwo/YmA3ZlsHpFcA4CbatRGae7Y 3Hqcdz2zh+B7wLo= =r4Ob -----END PGP SIGNATURE----- gpgv: Signature made Fri Dec 2 17:12:51 2022 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./iva_1.0.11+ds-3.dsc dpkg-source: info: extracting iva in /<> dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.11+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-24893442 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24893442 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24893442 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /<>/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:240: python3.10 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>' chmod a-x /<>/iva/read_trim/adapters.fasta chmod a+x /<>/iva/gage/getCorrectnessStats.sh chmod a+x /<>/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /<>/iva/gage/*.java [parsing started SimpleFileObject[/<>/iva/gage/GetFastaStats.java]] [parsing completed 204ms] [parsing started SimpleFileObject[/<>/iva/gage/SizeFasta.java]] [parsing completed 22ms] [parsing started SimpleFileObject[/<>/iva/gage/SplitFastaByLetter.java]] [parsing completed 13ms] [parsing started SimpleFileObject[/<>/iva/gage/Utils.java]] [parsing completed 53ms] [parsing started SimpleFileObject[/<>/iva/gage/getScaffoldStats.java]] [parsing completed 103ms] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.random/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.incubator.foreign/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-17-openjdk-armhf/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/constant/Constable.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/lang/constant/ConstantDesc.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/util/Iterator.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [wrote /<>/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /<>/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /<>/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /<>/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/util/Optional.class] [loading /modules/java.base/java/lang/Enum$EnumDesc.class] [loading /modules/java.base/java/lang/constant/DynamicConstantDesc.class] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/invoke/TypeDescriptor.class] [loading /modules/java.base/java/lang/invoke/TypeDescriptor$OfField.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /<>/iva/gage/Utils$Pair.class] [wrote /<>/iva/gage/Utils$Translate.class] [wrote /<>/iva/gage/Utils$ToProtein.class] [wrote /<>/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /<>/iva/gage/getScaffoldStats$Scaffold.class] [wrote /<>/iva/gage/getScaffoldStats.class] [total 5033ms] dh_auto_build -- I: pybuild base:240: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/read_trim.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/external_progs.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/common.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/egg_extract.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/qc_external.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/kmers.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/contig_trim.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/qc.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/edge.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/mapping.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/mummer.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/seed_processor.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/graph.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/assembly.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/seed.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/contig.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/__init__.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/test_data_runner.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/kraken.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva copying iva/kcount.py -> /<>/.pybuild/cpython3_3.10_iva/build/iva creating /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/.pybuild/cpython3_3.10_iva/build/iva/gage creating /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt creating /<>/.pybuild/cpython3_3.10_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/.pybuild/cpython3_3.10_iva/build/iva/read_trim creating /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.10 copying and adjusting scripts/iva_qc -> build/scripts-3.10 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.10 copying and adjusting scripts/iva -> build/scripts-3.10 changing mode of build/scripts-3.10/iva_qc from 644 to 755 changing mode of build/scripts-3.10/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.10/iva from 644 to 755 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' python3 -m pytest --verbose ============================= test session starts ============================== platform linux -- Python 3.10.8, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /<> collecting ... collected 160 items iva/tests/assembly_test.py::TestAssembly::test_contig_contained_in_nucmer_hits PASSED [ 0%] iva/tests/assembly_test.py::TestAssembly::test_contig_names_size_order PASSED [ 1%] iva/tests/assembly_test.py::TestAssembly::test_contig_worth_extending PASSED [ 1%] iva/tests/assembly_test.py::TestAssembly::test_coords_to_new_contig PASSED [ 2%] iva/tests/assembly_test.py::TestAssembly::test_extend_contigs_with_bam PASSED [ 3%] iva/tests/assembly_test.py::TestAssembly::test_get_contig_order_by_orfs PASSED [ 3%] iva/tests/assembly_test.py::TestAssembly::test_get_ref_length PASSED [ 4%] iva/tests/assembly_test.py::TestAssembly::test_get_ref_length_sam_pair PASSED [ 5%] iva/tests/assembly_test.py::TestAssembly::test_get_unmapped_pairs PASSED [ 5%] iva/tests/assembly_test.py::TestAssembly::test_good_intervals_from_strand_coverage PASSED [ 6%] iva/tests/assembly_test.py::TestAssembly::test_init_and_write PASSED [ 6%] iva/tests/assembly_test.py::TestAssembly::test_map_reads PASSED [ 7%] iva/tests/assembly_test.py::TestAssembly::test_merge_overlapping_contigs PASSED [ 8%] iva/tests/assembly_test.py::TestAssembly::test_read_pair_extend PASSED [ 8%] iva/tests/assembly_test.py::TestAssembly::test_remove_contained_contigs PASSED [ 9%] iva/tests/assembly_test.py::TestAssembly::test_remove_contig PASSED [ 10%] iva/tests/assembly_test.py::TestAssembly::test_remove_contig_from_nucmer_hits PASSED [ 10%] iva/tests/assembly_test.py::TestAssembly::test_subcontigs_from_strand_bias PASSED [ 11%] iva/tests/assembly_test.py::TestAssembly::test_trim_contig_for_strand_bias PASSED [ 11%] iva/tests/assembly_test.py::TestAssembly::test_trim_contigs PASSED [ 12%] iva/tests/assembly_test.py::TestAssembly::test_trim_strand_biased_ends PASSED [ 13%] iva/tests/assembly_test.py::TestAssembly::test_worth_extending PASSED [ 13%] iva/tests/contig_test.py::TestContig::test_add_left_kmer PASSED [ 14%] iva/tests/contig_test.py::TestContig::test_add_right_kmer PASSED [ 15%] iva/tests/contig_test.py::TestContig::test_extend PASSED [ 15%] iva/tests/contig_test.py::TestContig::test_init PASSED [ 16%] iva/tests/contig_test.py::TestContig::test_len PASSED [ 16%] iva/tests/contig_trim_test.py::TestContigTrim::test_coverage_to_trimmed_coords PASSED [ 17%] iva/tests/contig_trim_test.py::TestContigTrim::test_trim_ends PASSED [ 18%] iva/tests/contig_trim_test.py::TestContigTrim::test_trim_primers_and_adapters PASSED [ 18%] iva/tests/edge_test.py::TestEdge::test_change_hit_coords_with_intersection PASSED [ 19%] iva/tests/edge_test.py::TestEdge::test_make_contig_first PASSED [ 20%] iva/tests/edge_test.py::TestEdge::test_make_contig_forwards PASSED [ 20%] iva/tests/edge_test.py::TestEdge::test_merge_into PASSED [ 21%] iva/tests/edge_test.py::TestEdge::test_open_end PASSED [ 21%] iva/tests/edge_test.py::TestEdge::test_reverse PASSED [ 22%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir PASSED [ 23%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_unzipped PASSED [ 23%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_zipped PASSED [ 24%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file PASSED [ 25%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_unzipped PASSED [ 25%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_zipped PASSED [ 26%] iva/tests/egg_extract_test.py::TestEggExtract::test_init_and_write PASSED [ 26%] iva/tests/external_progs_test.py::TestExternalProgs::test_blastn_version PASSED [ 27%] iva/tests/external_progs_test.py::TestExternalProgs::test_delta_filter_in_path PASSED [ 28%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_in_path PASSED [ 28%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_version PASSED [ 29%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_in_path PASSED [ 30%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_version PASSED [ 30%] iva/tests/external_progs_test.py::TestExternalProgs::test_makeblastdb_version PASSED [ 31%] iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_in_path PASSED [ 31%] iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED [ 32%] iva/tests/external_progs_test.py::TestExternalProgs::test_r_version PASSED [ 33%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_in_path PASSED [ 33%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 34%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_version PASSED [ 35%] iva/tests/external_progs_test.py::TestExternalProgs::test_show_coords_in_path PASSED [ 35%] iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_in_path PASSED [ 36%] iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_version PASSED [ 36%] iva/tests/graph_test.py::TestGraph::test_add_and_get_edges PASSED [ 37%] iva/tests/graph_test.py::TestGraph::test_connected_components PASSED [ 38%] iva/tests/graph_test.py::TestGraph::test_degree PASSED [ 38%] iva/tests/graph_test.py::TestGraph::test_edges_are_consistent PASSED [ 39%] iva/tests/graph_test.py::TestGraph::test_find_simple_path PASSED [ 40%] iva/tests/graph_test.py::TestGraph::test_get_nodes PASSED [ 40%] iva/tests/graph_test.py::TestGraph::test_merged_coords_from_simple_nonredundant_path PASSED [ 41%] iva/tests/graph_test.py::TestGraph::test_node_to_coords PASSED [ 41%] iva/tests/graph_test.py::TestGraph::test_remove_middle_node PASSED [ 42%] iva/tests/graph_test.py::TestGraph::test_remove_node PASSED [ 43%] iva/tests/graph_test.py::TestGraph::test_remove_redundant_nodes_from_simple_path PASSED [ 43%] iva/tests/graph_test.py::TestGraph::test_simple_path_is_consistent PASSED [ 44%] iva/tests/kcount_test.py::TestKcount::test_counts_file_to_fasta PASSED [ 45%] iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fa PASSED [ 45%] iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fq PASSED [ 46%] iva/tests/kcount_test.py::TestKcount::test_kmc_to_kmer_counts PASSED [ 46%] iva/tests/kcount_test.py::TestKcount::test_median PASSED [ 47%] iva/tests/kmers_test.py::TestKmers::test_append PASSED [ 48%] iva/tests/kmers_test.py::TestKmers::test_commonest_kmers PASSED [ 48%] iva/tests/kmers_test.py::TestKmers::test_extend PASSED [ 49%] iva/tests/kmers_test.py::TestKmers::test_extension PASSED [ 50%] iva/tests/kmers_test.py::TestKmers::test_init PASSED [ 50%] iva/tests/kmers_test.py::TestKmers::test_kmer_dict PASSED [ 51%] iva/tests/kraken_test.py::TestKraken::test_append_to_file PASSED [ 51%] iva/tests/kraken_test.py::TestKraken::test_count_cds_from_embl PASSED [ 52%] iva/tests/kraken_test.py::TestKraken::test_genbank_to_taxon_and_gi PASSED [ 53%] iva/tests/kraken_test.py::TestKraken::test_get_most_common_species_dir PASSED [ 53%] iva/tests/kraken_test.py::TestKraken::test_get_parent_taxons PASSED [ 54%] iva/tests/kraken_test.py::TestKraken::test_load_extra_ref_info PASSED [ 55%] iva/tests/kraken_test.py::TestKraken::test_replace_fasta_header PASSED [ 55%] iva/tests/kraken_test.py::TestKraken::test_species_to_dir PASSED [ 56%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files PASSED [ 56%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files_region PASSED [ 57%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_region_fasta PASSED [ 58%] iva/tests/mapping_test.py::TestMapping::test_bam_to_fasta PASSED [ 58%] iva/tests/mapping_test.py::TestMapping::test_can_extend PASSED [ 59%] iva/tests/mapping_test.py::TestMapping::test_consensus_base PASSED [ 60%] iva/tests/mapping_test.py::TestMapping::test_consensus_base_both_strands PASSED [ 60%] iva/tests/mapping_test.py::TestMapping::test_find_incorrect_ref_bases PASSED [ 61%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd PASSED [ 61%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd_And_rev PASSED [ 62%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_rev PASSED [ 63%] iva/tests/mapping_test.py::TestMapping::test_get_pair_type PASSED [ 63%] iva/tests/mapping_test.py::TestMapping::test_get_ref_name PASSED [ 64%] iva/tests/mapping_test.py::TestMapping::test_map_reads PASSED [ 65%] iva/tests/mapping_test.py::TestMapping::test_map_reads_and_sort PASSED [ 65%] iva/tests/mapping_test.py::TestMapping::test_map_reads_wth_flag PASSED [ 66%] iva/tests/mapping_test.py::TestMapping::test_remove_indels PASSED [ 66%] iva/tests/mapping_test.py::TestMapping::test_sam_to_fasta PASSED [ 67%] iva/tests/mapping_test.py::TestMapping::test_smalt_in_path PASSED [ 68%] iva/tests/mapping_test.py::TestMapping::test_soft_clipped PASSED [ 68%] iva/tests/mapping_test.py::TestMapping::test_strip_mpileup_coverage_string PASSED [ 69%] iva/tests/mapping_test.py::TestMapping::test_total_ref_length_from_bam PASSED [ 70%] iva/tests/mummer_test.py::TestMummer::test_file_read PASSED [ 70%] iva/tests/mummer_test.py::TestMummer::test_is_at_ends PASSED [ 71%] iva/tests/mummer_test.py::TestMummer::test_is_self_hit PASSED [ 71%] iva/tests/mummer_test.py::TestMummer::test_on_same_strand PASSED [ 72%] iva/tests/mummer_test.py::TestMummer::test_qry_coords PASSED [ 73%] iva/tests/mummer_test.py::TestMummer::test_ref_coords PASSED [ 73%] iva/tests/mummer_test.py::TestMummer::test_run_nucmer PASSED [ 74%] iva/tests/mummer_test.py::TestMummer::test_sort PASSED [ 75%] iva/tests/mummer_test.py::TestMummer::test_swap PASSED [ 75%] iva/tests/mummer_test.py::TestMummer::test_to_graph_edge PASSED [ 76%] iva/tests/qc_external_test.py::TestQcExternal::test_run_gage PASSED [ 76%] iva/tests/qc_external_test.py::TestQcExternal::test_run_ratt PASSED [ 77%] iva/tests/qc_test.py::TestQc::test_calculate_cds_assembly_stats PASSED [ 78%] iva/tests/qc_test.py::TestQc::test_calculate_contig_placement PASSED [ 78%] iva/tests/qc_test.py::TestQc::test_calculate_ref_positions_covered_by_contigs PASSED [ 79%] iva/tests/qc_test.py::TestQc::test_calculate_ref_read_coverage PASSED [ 80%] iva/tests/qc_test.py::TestQc::test_calculate_ref_read_region_coverage PASSED [ 80%] iva/tests/qc_test.py::TestQc::test_calculate_refseq_assembly_stats PASSED [ 81%] iva/tests/qc_test.py::TestQc::test_calculate_should_have_assembled PASSED [ 81%] iva/tests/qc_test.py::TestQc::test_contig_placement_in_reference PASSED [ 82%] iva/tests/qc_test.py::TestQc::test_contigs_and_bases_that_hit_ref PASSED [ 83%] iva/tests/qc_test.py::TestQc::test_cov_to_R_string PASSED [ 83%] iva/tests/qc_test.py::TestQc::test_coverage_list_to_low_cov_intervals PASSED [ 84%] iva/tests/qc_test.py::TestQc::test_get_R_plot_contig_order_from_contig_placement PASSED [ 85%] iva/tests/qc_test.py::TestQc::test_get_contig_hits_to_reference PASSED [ 85%] iva/tests/qc_test.py::TestQc::test_get_overlapping_qry_hits PASSED [ 86%] iva/tests/qc_test.py::TestQc::test_get_ref_cds_from_gff PASSED [ 86%] iva/tests/qc_test.py::TestQc::test_get_unique_and_repetitive_from_contig_hits PASSED [ 87%] iva/tests/qc_test.py::TestQc::test_gff_and_fasta_to_cds PASSED [ 88%] iva/tests/qc_test.py::TestQc::test_has_orf PASSED [ 88%] iva/tests/qc_test.py::TestQc::test_hash_nucmer_hits_by_ref PASSED [ 89%] iva/tests/qc_test.py::TestQc::test_ids_in_order_from_fai PASSED [ 90%] iva/tests/qc_test.py::TestQc::test_invert_list PASSED [ 90%] iva/tests/qc_test.py::TestQc::test_map_cds_to_assembly PASSED [ 91%] iva/tests/qc_test.py::TestQc::test_mummer_coords_file_to_dict PASSED [ 91%] iva/tests/qc_test.py::TestQc::test_write_cds_seqs PASSED [ 92%] iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_hit_ref PASSED [ 93%] iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_not_hit_ref PASSED [ 93%] iva/tests/qc_test.py::TestQc::test_write_ref_coverage_to_files_for_R PASSED [ 94%] iva/tests/read_trim_test.py::TestReadTrim::test_run_trimmomatic PASSED [ 95%] iva/tests/seed_test.py::TestSeed::test_extend PASSED [ 95%] iva/tests/seed_test.py::TestSeed::test_extend_with_reads_as_single_end PASSED [ 96%] iva/tests/seed_test.py::TestSeed::test_extension_from_read PASSED [ 96%] iva/tests/seed_test.py::TestSeed::test_extensions_from_reads_file PASSED [ 97%] iva/tests/seed_test.py::TestSeed::test_init PASSED [ 98%] iva/tests/seed_test.py::TestSeed::test_kmc_in_path PASSED [ 98%] iva/tests/seed_test.py::TestSeed::test_len PASSED [ 99%] iva/tests/seed_test.py::TestSeed::test_write_fasta PASSED [100%] =============================== warnings summary =============================== iva/mapping.py:161 /<>/iva/mapping.py:161: DeprecationWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) iva/external_progs.py:33 /<>/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /<>/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /<>/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /<>/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /<>/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/external_progs.py:19 /<>/iva/external_progs.py:19: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.version import LooseVersion ../../../usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:346 /usr/lib/python3/dist-packages/networkx/readwrite/graphml.py:346: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations (np.int, "int"), (np.int8, "int"), ../../../usr/lib/python3/dist-packages/networkx/readwrite/gexf.py:223 /usr/lib/python3/dist-packages/networkx/readwrite/gexf.py:223: DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To silence this warning, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information. Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations (np.int, "int"), (np.int8, "int"), iva/kraken.py:360 /<>/iva/kraken.py:360: DeprecationWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /<>/iva/kraken.py:415: DeprecationWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /<>/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ====================== 160 passed, 12 warnings in 12.95s ======================= make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/iva/ -a -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_scripts running install_lib creating /<>/debian/iva/usr creating /<>/debian/iva/usr/lib creating /<>/debian/iva/usr/lib/python3.10 creating /<>/debian/iva/usr/lib/python3.10/dist-packages creating /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/read_trim.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/external_progs.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats.java -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/SizeFasta.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$Translate.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$ToProtein.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/getScaffoldStats.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils$Pair.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats.java -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/SizeFasta.java -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/SplitFastaByLetter.java -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/colsum.pl -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/GetFastaStats.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/getMummerStats.sh -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/SplitFastaByLetter.class -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/getCorrectnessStats.sh -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.10_iva/build/iva/gage/Utils.java -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/gage creating /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reference.fasta -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reads_1.fq.gz -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/reads_2.fq.gz -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.10_iva/build/iva/common.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/egg_extract.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/qc_external.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/kmers.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/contig_trim.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/qc.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/edge.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/mapping.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/genbank2embl.pl -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt.config.hiv -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt.config -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/embl2gff.pl -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/main.ratt.pl -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/start.ratt.sh -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/ratt/ratt_correction.pm -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.10_iva/build/iva/mummer.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/seed_processor.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/graph.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/assembly.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/seed.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.10_iva/build/iva/read_trim/adapters.fasta -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.10_iva/build/iva/contig.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/__init__.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/test_data_runner.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/kraken.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva copying /<>/.pybuild/cpython3_3.10_iva/build/iva/kcount.py -> /<>/debian/iva/usr/lib/python3.10/dist-packages/iva byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/read_trim.py to read_trim.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/external_progs.py to external_progs.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/common.py to common.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/egg_extract.py to egg_extract.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/qc_external.py to qc_external.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/kmers.py to kmers.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/contig_trim.py to contig_trim.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/qc.py to qc.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/edge.py to edge.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/mapping.py to mapping.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/mummer.py to mummer.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/seed_processor.py to seed_processor.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/graph.py to graph.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/assembly.py to assembly.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/seed.py to seed.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/contig.py to contig.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/kraken.py to kraken.cpython-310.pyc byte-compiling /<>/debian/iva/usr/lib/python3.10/dist-packages/iva/kcount.py to kcount.cpython-310.pyc running install_egg_info running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /<>/debian/iva/usr/lib/python3.10/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/iva/usr/bin copying build/scripts-3.10/iva_qc -> /<>/debian/iva/usr/bin copying build/scripts-3.10/iva_qc_make_db -> /<>/debian/iva/usr/bin copying build/scripts-3.10/iva -> /<>/debian/iva/usr/bin changing mode of /<>/debian/iva/usr/bin/iva_qc to 755 changing mode of /<>/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /<>/debian/iva/usr/bin/iva to 755 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man PYTHONPATH=. help2man -N -o /<>/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /<>/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /<>/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/<>' dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 149 pkgstriptranslations: processing iva (in debian/iva); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/iva/DEBIAN/control, package iva, directory debian/iva pkgstripfiles: Running PNG optimization (using 4 cpus) for package iva ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iva' in '../iva_1.0.11+ds-3_armhf.deb'. dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-3_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../iva_1.0.11+ds-3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-02T23:26:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.11+ds-3_armhf.changes: ------------------------------ Format: 1.8 Date: Fri, 02 Dec 2022 17:51:23 +0100 Source: iva Binary: iva Built-For-Profiles: noudeb Architecture: armhf Version: 1.0.11+ds-3 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: iva - iterative virus sequence assembler Closes: 1018382 Changes: iva (1.0.11+ds-3) unstable; urgency=medium . * Team upload. * d/control: replace nose by pytest. (Closes: #1018382) * d/rules: fetch and run tests with pytest-3. * Set upstream metadata fields: Repository-Browse. Checksums-Sha1: 5c27b3888af7aa2f7b12ef6b1aee11a279e85bc4 8858 iva_1.0.11+ds-3_armhf.buildinfo e22f877ffc5267f0eb2fdcc19bfb3bf00babf025 8581828 iva_1.0.11+ds-3_armhf.deb Checksums-Sha256: b0a67faaee3144d08cabd31479da77faed3a54aa2a4d49a5d233d5b994ec75ff 8858 iva_1.0.11+ds-3_armhf.buildinfo 45a9b6138c3cd1fa4e8ce4e77688efee9f22e096b32bd1b5609c720ddd6124c9 8581828 iva_1.0.11+ds-3_armhf.deb Files: 9cc240862c67d630d1d094bb1173fa6b 8858 science optional iva_1.0.11+ds-3_armhf.buildinfo 33a759f1ea894a00f8d5df3c5d36fa03 8581828 science optional iva_1.0.11+ds-3_armhf.deb /<>/iva_1.0.11+ds-3_armhf.changes.new could not be renamed to /<>/iva_1.0.11+ds-3_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iva Binary: iva Architecture: armhf Version: 1.0.11+ds-3 Checksums-Md5: 33a759f1ea894a00f8d5df3c5d36fa03 8581828 iva_1.0.11+ds-3_armhf.deb Checksums-Sha1: e22f877ffc5267f0eb2fdcc19bfb3bf00babf025 8581828 iva_1.0.11+ds-3_armhf.deb Checksums-Sha256: 45a9b6138c3cd1fa4e8ce4e77688efee9f22e096b32bd1b5609c720ddd6124c9 8581828 iva_1.0.11+ds-3_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Fri, 02 Dec 2022 23:26:15 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39-8ubuntu2), binutils-arm-linux-gnueabihf (= 2.39-8ubuntu2), binutils-common (= 2.39-8ubuntu2), bioperl (= 1.7.8-1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), ca-certificates-java (= 20220719), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-9ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.80), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), default-jdk-headless (= 2:1.17-73), default-jre-headless (= 2:1.17-73), dh-autoreconf (= 20), dh-python (= 5.20221122), dh-strip-nondeterminism (= 1.13.0-2), diffutils (= 1:3.8-1), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14+20220924-2), fastaq (= 3.17.0-5), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), fontconfig-config (= 2.13.1-4.4ubuntu1), fonts-dejavu-core (= 2.37-2build1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-9ubuntu1), gawk (= 1:5.1.0-1build3), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-9ubuntu1), gcc-12-base (= 12.2.0-9ubuntu1), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), help2man (= 1.49.2), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), java-common (= 0.73), kmc (= 3.2.1+dfsg-1), libacl1 (= 2.3.1-1), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-9ubuntu1), libasound2 (= 1.2.8-1), libasound2-data (= 1.2.8-1), libatomic1 (= 12.2.0-9ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libavahi-client3 (= 0.8-6ubuntu1), libavahi-common-data (= 0.8-6ubuntu1), libavahi-common3 (= 0.8-6ubuntu1), libbambamc0 (= 0.0.50-6), libbinutils (= 2.39-8ubuntu2), libbio-perl-perl (= 1.7.8-1), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.36-0ubuntu4), libc-dev-bin (= 2.36-0ubuntu4), libc6 (= 2.36-0ubuntu4), libc6-dev (= 2.36-0ubuntu4), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.44-1build3), libcapture-tiny-perl (= 0.48-1), libcc1-0 (= 12.2.0-9ubuntu1), libclass-data-inheritable-perl (= 0.08-3), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39-8ubuntu2), libctf0 (= 2.39-8ubuntu2), libcups2 (= 2.4.2-1ubuntu2), libcurl3-gnutls (= 7.86.0-2), libdata-stag-perl (= 0.14-3), libdb5.3 (= 5.3.28+dfsg1-0.10), libdbus-1-3 (= 1.14.0-2ubuntu3), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.10.1ubuntu1), libdeflate0 (= 1.14-1), libdevel-stacktrace-perl (= 2.0400-2), libdpkg-perl (= 1.21.9ubuntu1), libdw1 (= 0.188-1), libelf1 (= 0.188-1), libexception-class-perl (= 1.45-1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.0-2), libfontconfig1 (= 2.13.1-4.4ubuntu1), libfreetype6 (= 2.12.1+dfsg-3), libgcc-12-dev (= 12.2.0-9ubuntu1), libgcc-s1 (= 12.2.0-9ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 12.2.0-9ubuntu1), libglib2.0-0 (= 2.74.2-1), libgmp10 (= 2:6.2.1+dfsg1-1ubuntu2), libgnutls30 (= 3.7.7-2ubuntu2), libgomp1 (= 12.2.0-9ubuntu1), libgpg-error0 (= 1.46-1), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.20.1-1), libharfbuzz0b (= 5.2.0-2), libhogweed6 (= 3.8.1-2), libhts3 (= 1.16+ds-3), libhtscodecs2 (= 1.3.0-4), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libio-string-perl (= 1.08-3.1), libisl23 (= 0.25-1), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libk5crypto3 (= 1.20.1-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20.1-1), libkrb5support0 (= 1.20.1-1), liblapack3 (= 3.11.0-2), liblcms2-2 (= 2.13.1-1), libldap-2.5-0 (= 2.5.13+dfsg-1ubuntu1), liblocale-gettext-perl (= 1.07-4build4), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.2.8-0.0), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.50.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnspr4 (= 2:4.35-1), libnss3 (= 2:3.85-1), libp11-kit0 (= 0.24.1-1ubuntu2), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.40-1ubuntu1), libpcsclite1 (= 1.9.9-1), libperl5.36 (= 5.36.0-4ubuntu2), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.39-2), libpsl5 (= 0.21.0-1.2build2), libpython3-stdlib (= 3.10.6-1ubuntu1), libpython3.10-minimal (= 3.10.8-3), libpython3.10-stdlib (= 3.10.8-3), libpython3.11-minimal (= 3.11.0-3), libpython3.11-stdlib (= 3.11.0-3), libreadline8 (= 8.2-1.2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-6ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu2), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build1), libsigsegv2 (= 2.14-1ubuntu1), libsmartcols1 (= 2.38.1-4ubuntu1), libsqlite3-0 (= 3.40.0-1), libssh-4 (= 0.10.4-2), libssl-dev (= 3.0.5-2ubuntu2), libssl3 (= 3.0.5-2ubuntu2), libstdc++-12-dev (= 12.2.0-9ubuntu1), libstdc++6 (= 12.2.0-9ubuntu1), libsub-override-perl (= 0.09-4), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 251.4-1ubuntu7), libtasn1-6 (= 4.19.0-2), libtest-deep-perl (= 1.130-2), libtest-differences-perl (= 0.69-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libubsan1 (= 12.2.0-9ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.4-1ubuntu7), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 36), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), mummer (= 3.23+dfsg-7), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), openjdk-17-jdk-headless (= 17.0.5+8-2ubuntu1), openjdk-17-jre-headless (= 17.0.5+8-2ubuntu1), openssl (= 3.0.5-2ubuntu2), patch (= 2.7.6-7build2), perl (= 5.36.0-4ubuntu2), perl-base (= 5.36.0-4ubuntu2), perl-modules-5.36 (= 5.36.0-4ubuntu2), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.6-1ubuntu1), python3-attr (= 22.1.0-1), python3-decorator (= 4.4.2-0ubuntu1), python3-distutils (= 3.10.8-1), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.10.8-1), python3-minimal (= 3.10.6-1ubuntu1), python3-more-itertools (= 8.10.0-2), python3-networkx (= 2.4-4ubuntu2), python3-numpy (= 1:1.21.5-1ubuntu1), python3-packaging (= 21.3-1.1), python3-pkg-resources (= 65.5.0-1), python3-pluggy (= 1.0.0+repack-1), python3-py (= 1.11.0-1), python3-pyparsing (= 3.0.7-3), python3-pysam (= 0.20.0+ds-1), python3-pytest (= 7.1.2-2ubuntu1), python3-setuptools (= 65.5.0-1), python3-tomli (= 2.0.1-1), python3.10 (= 3.10.8-3), python3.10-minimal (= 3.10.8-3), python3.11 (= 3.11.0-3), python3.11-minimal (= 3.11.0-3), readline-common (= 8.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.16.1-1), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), smalt (= 0.7.6-12), sysvinit-utils (= 3.05-7ubuntu1), tar (= 1.34+dfsg-1.1), ucf (= 3.0043), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), xz-utils (= 5.2.8-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1669999883" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iva_1.0.11+ds-3_armhf.deb ------------------------- new Debian package, version 2.0. size 8581828 bytes: control archive=2965 bytes. 1030 bytes, 22 lines control 5477 bytes, 64 lines md5sums 253 bytes, 12 lines * postinst #!/bin/sh 366 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.11+ds-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8766 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/iva Description: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. drwxr-xr-x root/root 0 2022-12-02 16:51 ./ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/bin/ -rwxr-xr-x root/root 17240 2022-12-02 16:51 ./usr/bin/iva -rwxr-xr-x root/root 6228 2022-12-02 16:51 ./usr/bin/iva_qc -rwxr-xr-x root/root 2406 2022-12-02 16:51 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/ -rw-r--r-- root/root 488 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt -rw-r--r-- root/root 4 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ -rw-r--r-- root/root 1033 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/__init__.py -rw-r--r-- root/root 29056 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/assembly.py -rw-r--r-- root/root 1856 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/common.py -rw-r--r-- root/root 1960 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig.py -rw-r--r-- root/root 4391 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig_trim.py -rw-r--r-- root/root 4903 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/edge.py -rw-r--r-- root/root 3077 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/egg_extract.py -rw-r--r-- root/root 4110 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- root/root 508 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class -rw-r--r-- root/root 10213 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class -rw-r--r-- root/root 14839 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java -rw-r--r-- root/root 3689 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class -rw-r--r-- root/root 3611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java -rw-r--r-- root/root 2898 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class -rw-r--r-- root/root 2229 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java -rw-r--r-- root/root 640 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class -rw-r--r-- root/root 4727 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class -rw-r--r-- root/root 1303 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class -rw-r--r-- root/root 5920 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/Utils.class -rw-r--r-- root/root 9230 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/Utils.java -rwxr-xr-x root/root 80 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl -rwxr-xr-x root/root 1773 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh -rwxr-xr-x root/root 1430 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh -rw-r--r-- root/root 814 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class -rw-r--r-- root/root 13712 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class -rw-r--r-- root/root 19111 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java -rw-r--r-- root/root 7133 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/graph.py -rw-r--r-- root/root 9487 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kcount.py -rw-r--r-- root/root 3466 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kmers.py -rw-r--r-- root/root 16961 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/kraken.py -rw-r--r-- root/root 13330 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/mapping.py -rw-r--r-- root/root 8365 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/mummer.py -rw-r--r-- root/root 36646 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/qc.py -rw-r--r-- root/root 8190 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/qc_external.py drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ratt/ -rwxr-xr-x root/root 1008 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl -rwxr-xr-x root/root 1045 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl -rwxr-xr-x root/root 41988 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl -rw-r--r-- root/root 90 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config -rw-r--r-- root/root 90 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv -rw-r--r-- root/root 57611 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm -rwxr-xr-x root/root 13201 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh -rw-r--r-- root/root 1428 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/read_trim.py drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/read_trim/ -rw-r--r-- root/root 3143 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta -rw-r--r-- root/root 6056 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/seed.py -rw-r--r-- root/root 5586 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/seed_processor.py -rw-r--r-- root/root 2443 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_data_runner.py drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/test_run_data/ -rw-r--r-- root/root 672 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa -rw-r--r-- root/root 9981 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -rw-r--r-- root/root 9200 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -rw-r--r-- root/root 3813239 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz -rw-r--r-- root/root 4661713 2022-12-02 16:51 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz -rw-r--r-- root/root 9217 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/doc/iva/ -rw-r--r-- root/root 1024 2022-12-02 16:51 ./usr/share/doc/iva/changelog.Debian.gz -rw-r--r-- root/root 1493 2022-12-02 16:51 ./usr/share/doc/iva/copyright drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/man/ drwxr-xr-x root/root 0 2022-12-02 16:51 ./usr/share/man/man1/ -rw-r--r-- root/root 2252 2022-12-02 16:51 ./usr/share/man/man1/iva.1.gz -rw-r--r-- root/root 1282 2022-12-02 16:51 ./usr/share/man/man1/iva_qc.1.gz -rw-r--r-- root/root 641 2022-12-02 16:51 ./usr/share/man/man1/iva_qc_make_db.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 37480 Build-Time: 62 Distribution: lunar-proposed Host Architecture: armhf Install-Time: 103 Job: iva_1.0.11+ds-3.dsc Machine Architecture: arm64 Package: iva Package-Time: 169 Source-Version: 1.0.11+ds-3 Space: 37480 Status: successful Version: 1.0.11+ds-3 -------------------------------------------------------------------------------- Finished at 2022-12-02T23:26:16Z Build needed 00:02:49, 37480k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=armhf PACKAGEBUILD-24893442 Scanning for processes to kill in build PACKAGEBUILD-24893442