sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | iva 1.0.11+ds-5 (amd64) Sun, 15 Sep 2024 12:11:25 +0000 | +==============================================================================+ Package: iva Version: 1.0.11+ds-5 Source Version: 1.0.11+ds-5 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-a23d9855-1594-49d9-b9f7-8d05c1fa72d9' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup iva_1.0.11+ds-5 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup iva_1.0.11+ds-5 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/iva-tiulQN/resolver-3CsDPM' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/iva_1.0.11+ds-5.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/iva-tiulQN/iva-1.0.11+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-tiulQN' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libssl-dev, bioperl, fastaq, kmc, 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-sequence-python3, libssl-dev, bioperl, fastaq, kmc, 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [841 B] Get:5 copy:/<>/apt_archive ./ Packages [873 B] Fetched 2323 B in 0s (198 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 additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot fastaq file gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcom-err2 libcurl3t64-gnutls libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1t64 libexception-class-perl libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsigsegv2 libssh2-1t64 libssl-dev libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtirpc-common libtirpc3t64 libtool libuchardet0 libxml2 m4 man-db media-types mummer netbase openjdk-21-jdk-headless openjdk-21-jre-headless openssl po-debconf python3 python3-autocommand python3-inflect python3-iniconfig python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pysam python3-pytest python3-setuptools python3-typeguard python3-typing-extensions python3-zipp python3.12 python3.12-minimal samtools sensible-utils smalt tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make default-jre flit python3-build python3-installer python3-wheel gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libxml-sax-expatxs-perl krb5-doc krb5-user liblcms2-utils pcscd libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-21-demo openjdk-21-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 gfortran python-numpy-doc python3-dev python-setuptools-doc python3.12-venv python3.12-doc binfmt-support 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 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 libarchive-cpio-perl krb5-locales libgpm2 publicsuffix libltdl-dev libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 libmail-sendmail-perl python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdextrautils ca-certificates ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fakeroot fastaq file gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcom-err2 libcurl3t64-gnutls libdata-stag-perl libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libelf1t64 libexception-class-perl libexpat1 libfakeroot libfile-stripnondeterminism-perl libgfortran5 libgssapi-krb5-2 libhts3t64 libhtscodecs2 libicu72 libio-string-perl libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblocale-gettext-perl libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsigsegv2 libssh2-1t64 libssl-dev libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtirpc-common libtirpc3t64 libtool libuchardet0 libxml2 m4 man-db media-types mummer netbase openjdk-21-jdk-headless openjdk-21-jre-headless openssl po-debconf python3 python3-autocommand python3-inflect python3-iniconfig python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pysam python3-pytest python3-setuptools python3-typeguard python3-typing-extensions python3-zipp python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy sensible-utils smalt tzdata 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 193 MB/193 MB of archives. After this operation, 609 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [996 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.5-1+b1 [27.0 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:16 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.5-1+b1 [9884 B] Get:24 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.5-1+b1 [27.9 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:46 http://deb.debian.org/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 bioperl all 1.7.8-1 [246 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:65 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get:74 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.103-1 [1352 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.0-1 [55.4 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.5~6ea-1 [41.8 MB] Get:80 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get:81 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk-headless amd64 21.0.5~6ea-1 [82.8 MB] Get:82 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get:83 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-1 [42.2 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:89 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.1-1 [10.2 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240824 [109 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.0-2 [359 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.20-3 [653 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 kmc amd64 3.2.4+dfsg-1+b1 [1049 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-4 [837 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get:120 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get:121 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.2-1 [249 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 smalt amd64 0.7.6-13 [115 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 193 MB in 1s (149 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Preparing to unpack .../102-smalt_0.7.6-13_amd64.deb ... Unpacking smalt (0.7.6-13) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../103-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-8) ... Setting up java-common (0.76) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.36-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 15 12:11:46 UTC 2024. Universal Time is now: Sun Sep 15 12:11:46 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.36-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libnspr4:amd64 (2:4.35-1.1+b1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up libssl-dev:amd64 (3.3.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up libpcsclite1:amd64 (2.3.0-1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-4) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up mummer (3.23+dfsg-8) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up netbase (6.4) ... Configuration file '/etc/protocols' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Configuration file '/etc/services' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up openssl (3.3.2-1) ... Setting up kmc (3.2.4+dfsg-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnss3:amd64 (2:3.103-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libtest-exception-perl (0.43-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up openjdk-21-jre-headless:amd64 (21.0.5~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3) ... Setting up libpython3-stdlib:amd64 (3.12.5-1+b1) ... Setting up python3 (3.12.5-1+b1) ... Setting up python3-zipp (3.20.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.2-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up fastaq (3.17.0-6) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-networkx (3.2.1-4) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20240824) ... Processing triggers for libc-bin (2.40-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.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:ANF_Secure_Server_Root_CA.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.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:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.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_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.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: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 Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.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:Entrust_Root_Certification_Authority.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.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_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.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:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.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: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_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.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:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.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:SZAFIR_ROOT_CA2.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.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: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:TunTrust_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_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:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem done. Setting up openjdk-21-jdk-headless:amd64 (21.0.5~6ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up default-jdk-headless (2:1.21-76) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bioperl_1.7.8-1 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 ca-certificates_20240203 ca-certificates-java_20240118 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 default-jdk-headless_2:1.21-76 default-jre-headless_2:1.21-76 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 fastaq_3.17.0-6 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gawk_1:5.2.1-2+b1 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 help2man_1.49.3 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 java-common_0.76 kmc_3.2.4+dfsg-1+b1 libacl1_2.3.2-2 libalgorithm-diff-perl_1.201-1 libapt-pkg6.0t64_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-4 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbambamc0_0.0.50-6+b1 libbinutils_2.43.1-4 libbio-perl-perl_1.7.8-1 libblas3_3.12.0-3 libblkid1_2.40.2-8 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcapture-tiny-perl_0.48-2 libcc1-0_14.2.0-4 libclass-data-inheritable-perl_0.08-3 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libcurl3t64-gnutls_8.10.0-2 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate0_1.21-1 libdevel-stacktrace-perl_2.0500-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libexception-class-perl_1.45-1 libexpat1_2.6.3-1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-4 libgcc-s1_14.2.0-4 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-4 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-4 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-4 libicu72_72.1-5 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.27-1 libitm1_14.2.0-4 libjansson4_2.14-2+b2 libjpeg62-turbo_1:2.1.5-3 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libksba8_1.6.7-2 liblapack3_3.12.0-3 liblcms2-2_2.14-2+b1 libldap-2.5-0_2.5.18+dfsg-3+b1 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-4 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncurses6_6.5-2 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.63.0-1 libnghttp3-9_1.4.0-1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnpth0t64_1.6-3.1 libnsl2_1.3.0-3+b2 libnspr4_2:4.35-1.1+b1 libnss3_2:3.103-1 libp11-kit0_0.25.5-2 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libpcsclite1_2.3.0-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0-5 libpipeline1_1.5.8-1 libpsl5t64_0.21.2-1.1 libpython3-stdlib_3.12.5-1+b1 libpython3.12-minimal_3.12.6-1 libpython3.12-stdlib_3.12.6-1 libquadmath0_14.2.0-4 libreadline8t64_8.2-5 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-4 libsigsegv2_2.14-1+b1 libsmartcols1_2.40.2-8 libsqlite3-0_3.46.1-1 libssh2-1t64_1.11.0-7 libssl-dev_3.3.2-1 libssl3t64_3.3.2-1 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 libsub-uplevel-perl_0.2800-3 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtest-deep-perl_1.204-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-diff-perl_1.45-2 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtool_2.4.7-7 libtsan2_14.2.0-4 libubsan1_14.2.0-4 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mummer_3.23+dfsg-8 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openjdk-21-jdk-headless_21.0.5~6ea-1 openjdk-21-jre-headless_21.0.5~6ea-1 openssl_3.3.2-1 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 po-debconf_1.0.21+nmu1 python3_3.12.5-1+b1 python3-autocommand_2.2.2-3 python3-inflect_7.3.1-1 python3-iniconfig_1.1.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.0.2-1 python3-minimal_3.12.5-1+b1 python3-more-itertools_10.4.0-1 python3-networkx_3.2.1-4 python3-numpy_1:1.26.4+ds-11 python3-packaging_24.1-1 python3-pkg-resources_74.1.2-2 python3-pluggy_1.5.0-1 python3-pysam_0.22.1+ds-2+b1 python3-pytest_8.3.2-1 python3-setuptools_74.1.2-2 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-zipp_3.20.1-1 python3.12_3.12.6-1 python3.12-minimal_3.12.6-1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 samtools_1.20-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 smalt_0.7.6-13 sysvinit-utils_3.10-2 tar_1.35+dfsg-3 tzdata_2024a-4 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.11+ds-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.6.2 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-sequence-python3, libssl-dev, bioperl, fastaq, kmc, 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 30c67565ccddfecdcac0a5e1fe6da1278ef3481c 5992 iva_1.0.11+ds-5.debian.tar.xz Checksums-Sha256: 0835a11746deaa4067aeb1bc9817ed8d415f36de51ae4fc122ea5b287c5ecf1d 8680588 iva_1.0.11+ds.orig.tar.xz aea1686cc3a60ec0fbfd9340b5332cf0430cd814f96ae1ac6992cb8e6f8a6467 5992 iva_1.0.11+ds-5.debian.tar.xz Files: e7b6c8d9cc2adb23b0d90168122c33b3 8680588 iva_1.0.11+ds.orig.tar.xz 0ef1450aea819feff2cd1b7b0edb906a 5992 iva_1.0.11+ds-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW7k/0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEx8g/9GbdcWmPxrT733yvQimaZFg00Iy6yqAmj +K7oOvPXC4nkJ5Ft/5KR8bRueC3DIPLL5VmrttD14SICFi0Be8VcP8I4I7TOQi0z xkiC80VAIUSKJ9GDo+jMRWkB93bFnsnuCILAgC2b6eIfWeyGB4xX+qv/qqNpaY+s lIoHTpRXnIaWGWcxJfs132HoJeeUjWuqrt7UG7apx61aB0P3imVpZYFbvyvROuN5 zxnj0ga+hw/pqBikfRQCnQu1Me3aMOurE7Q42N2CSO8A2VCFzCX3DYGhRCFKZuE0 cTOxmwO88ZUN80fAbm7mTMOrQpwMFsMtbVEIHk6o8hx8IiUn43gbf1pMRaKLhKK8 BMncd8ME+zVpI8F/Ag5209h1Eawibwd+dM4J+cHN2ENe4M1P3Qc2bw4a5vhi2+H/ p0mhCyYpNG2XU0VnnoNhpCU5dLrX7mYaEbjR19y9A98kCFFqSQ6yJmIyC8icm5HI 9SVS0U6tU6qbC1jmhqI313VlYYN+qH5t1z71ktLo4Uq5khmdC/Qrv2XVhARkS+Tr ZmOMQGJIwgC0hkKFpuNtzcocTIlAQSyo7QQCPVsNYh//UCyk1RPO9Ta1LpsNQ0hN Q33gwdEqgMMrZW30A9qyR71bno5aRznYe8FeNt/razi5XHm5U2eipEcmwCEU4jN5 0Eq06ewO6c0= =RITE -----END PGP SIGNATURE----- gpgv: Signature made Thu Feb 1 12:52:13 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found 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-5.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 dpkg-source: info: applying python3.12.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network iva_1.0.11+ds-5 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network iva_1.0.11+ds-5 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-a23d9855-1594-49d9-b9f7-8d05c1fa72d9 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf .pybuild *.egg-info .pytest_cache build 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 dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building iva using existing ./iva_1.0.11+ds.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building iva in iva_1.0.11+ds-5.debian.tar.xz dpkg-source: info: building iva in iva_1.0.11+ds-5.dsc debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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 38ms] [parsing started SimpleFileObject[/<>/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/<>/iva/gage/SplitFastaByLetter.java]] [parsing completed 2ms] [parsing started SimpleFileObject[/<>/iva/gage/Utils.java]] [parsing completed 15ms] [parsing started SimpleFileObject[/<>/iva/gage/getScaffoldStats.java]] [parsing completed 13ms] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.random/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-21-openjdk-amd64/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/Appendable.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.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/SequencedCollection.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/jdk/internal/javac/PreviewFeature.class] [loading /modules/java.base/jdk/internal/javac/PreviewFeature$Feature.class] [loading /modules/java.base/jdk/internal/javac/PreviewFeature$JEP.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 934ms] Note: /<>/iva/gage/Utils.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. dh_auto_build -- I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) 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_3.12_iva/build/iva copying iva/graph.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mummer.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/__init__.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kcount.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/edge.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kraken.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/assembly.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc_external.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/common.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kmers.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/read_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mapping.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/egg_extract.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/external_progs.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/test_data_runner.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed_processor.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva creating /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage creating /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt creating /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim creating /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.12 copying and adjusting scripts/iva_qc -> build/scripts-3.12 copying and adjusting scripts/iva -> build/scripts-3.12 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.12 changing mode of build/scripts-3.12/iva_qc from 644 to 755 changing mode of build/scripts-3.12/iva from 644 to 755 changing mode of build/scripts-3.12/iva_qc_make_db 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 3.12.6, pytest-8.3.2, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /<> plugins: typeguard-4.3.0 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: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution iva/external_progs.py:33 /<>/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /<>/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /<>/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /<>/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /<>/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /<>/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /<>/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /<>/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 160 passed, 10 warnings in 3.69s ======================= make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/iva/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /<>/debian/iva /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying iva/gage/Utils$Translate.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage running build_scripts running install_lib creating /<>/debian/iva/usr creating /<>/debian/iva/usr/lib creating /<>/debian/iva/usr/lib/python3.12 creating /<>/debian/iva/usr/lib/python3.12/dist-packages creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/graph.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/mummer.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/contig.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/__init__.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kcount.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/edge.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kraken.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/assembly.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/qc_external.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Translate.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$ToProtein.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getMummerStats.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/colsum.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Pair.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getCorrectnessStats.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/contig_trim.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/seed.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/common.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kmers.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/mapping.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/egg_extract.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/external_progs.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_data_runner.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/start.ratt.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt_correction.pm -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/main.ratt.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config.hiv -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/genbank2embl.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/embl2gff.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/qc.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim/adapters.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.12_iva/build/iva/seed_processor.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_2.fq.gz -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_1.fq.gz -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reference.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/graph.py to graph.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/mummer.py to mummer.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/contig.py to contig.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/__init__.py to __init__.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kcount.py to kcount.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/edge.py to edge.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kraken.py to kraken.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/assembly.py to assembly.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/qc_external.py to qc_external.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/contig_trim.py to contig_trim.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/seed.py to seed.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/common.py to common.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kmers.py to kmers.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim.py to read_trim.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/mapping.py to mapping.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/egg_extract.py to egg_extract.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/external_progs.py to external_progs.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/qc.py to qc.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/seed_processor.py to seed_processor.cpython-312.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/python3.12/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/iva/usr/bin copying build/scripts-3.12/iva_qc -> /<>/debian/iva/usr/bin copying build/scripts-3.12/iva -> /<>/debian/iva/usr/bin copying build/scripts-3.12/iva_qc_make_db -> /<>/debian/iva/usr/bin changing mode of /<>/debian/iva/usr/bin/iva_qc to 755 changing mode of /<>/debian/iva/usr/bin/iva to 755 changing mode of /<>/debian/iva/usr/bin/iva_qc_make_db to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -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 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -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 -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'iva' in '../iva_1.0.11+ds-5_amd64.deb'. dpkg-genbuildinfo -O../iva_1.0.11+ds-5_amd64.buildinfo dpkg-genchanges -O../iva_1.0.11+ds-5_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-09-15T12:12:14Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.11+ds-5_amd64.changes: ------------------------------ Format: 1.8 Date: Thu, 01 Feb 2024 13:34:57 +0100 Source: iva Binary: iva Architecture: source amd64 Version: 1.0.11+ds-5 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: iva - iterative virus sequence assembler Closes: 1061804 Changes: iva (1.0.11+ds-5) unstable; urgency=medium . * Python3.12 compatibility by avoiding usage of distutils Closes: #1061804 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Remove patch reduce-ram.patch that is missing from debian/patches/series. 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9086d2acbcf03aa805a780b1007fac11 8581760 science optional iva_1.0.11+ds-5_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iva Binary: iva Architecture: amd64 source Version: 1.0.11+ds-5 Checksums-Md5: 603527c8e04e962634ab2045da0d54e8 1381 iva_1.0.11+ds-5.dsc 9086d2acbcf03aa805a780b1007fac11 8581760 iva_1.0.11+ds-5_amd64.deb Checksums-Sha1: 2fb9e2b2e196baa756d5183092204395e880aae6 1381 iva_1.0.11+ds-5.dsc ee28a3f0019f96a76f9f82da8923e737a3da84ff 8581760 iva_1.0.11+ds-5_amd64.deb Checksums-Sha256: dc142159ac7fcf9d8b737326e9a8a22cfb165560ebc610d073dcbc19faee749b 1381 iva_1.0.11+ds-5.dsc 1084a3377d6acdd79e8a1dbb1e6ecb14c35682aade67131b98a07018e4f1303b 8581760 iva_1.0.11+ds-5_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 15 Sep 2024 12:12:13 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bioperl (= 1.7.8-1), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), ca-certificates (= 20240203), ca-certificates-java (= 20240118), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-4), cpp-14-x86-64-linux-gnu (= 14.2.0-4), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), default-jdk-headless (= 2:1.21-76), default-jre-headless (= 2:1.21-76), dh-autoreconf (= 20), dh-python (= 6.20240824), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), fastaq (= 3.17.0-6), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-4), g++-14-x86-64-linux-gnu (= 14.2.0-4), g++-x86-64-linux-gnu (= 4:14.1.0-2), gawk (= 1:5.2.1-2+b1), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-4), gcc-14-base (= 14.2.0-4), gcc-14-x86-64-linux-gnu (= 14.2.0-4), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), gzip (= 1.12-1.1), help2man (= 1.49.3), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), java-common (= 0.76), kmc (= 3.2.4+dfsg-1+b1), libacl1 (= 2.3.2-2), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-4), libatomic1 (= 14.2.0-4), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbambamc0 (= 0.0.50-6+b1), libbinutils (= 2.43.1-4), libbio-perl-perl (= 1.7.8-1), libblas3 (= 3.12.0-3), libblkid1 (= 2.40.2-8), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14.2.0-4), libclass-data-inheritable-perl (= 0.08-3), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libcurl3t64-gnutls (= 8.10.0-2), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate0 (= 1.21-1), libdevel-stacktrace-perl (= 2.0500-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libexception-class-perl (= 1.45-1), libexpat1 (= 2.6.3-1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-4), libgcc-s1 (= 14.2.0-4), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran5 (= 14.2.0-4), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-4), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libio-string-perl (= 1.08-4), libisl23 (= 0.27-1), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), libjpeg62-turbo (= 1:2.1.5-3), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), liblapack3 (= 3.12.0-3), liblcms2-2 (= 2.14-2+b1), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), liblocale-gettext-perl (= 1.07-7+b1), liblsan0 (= 14.2.0-4), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libncurses6 (= 6.5-2), libncursesw6 (= 6.5-2), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.63.0-1), libnghttp3-9 (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libnsl2 (= 1.3.0-3+b2), libnspr4 (= 2:4.35-1.1+b1), libnss3 (= 2:3.103-1), libp11-kit0 (= 0.25.5-2), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libpcsclite1 (= 2.3.0-1), libperl5.40 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libpsl5t64 (= 0.21.2-1.1), libpython3-stdlib (= 3.12.5-1+b1), libpython3.12-minimal (= 3.12.6-1), libpython3.12-stdlib (= 3.12.6-1), libquadmath0 (= 14.2.0-4), libreadline8t64 (= 8.2-5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsigsegv2 (= 2.14-1+b1), libsmartcols1 (= 2.40.2-8), libsqlite3-0 (= 3.46.1-1), libssh2-1t64 (= 1.11.0-7), libssl-dev (= 3.3.2-1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 256.6-1), libtasn1-6 (= 4.19.0-3+b2), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-2), libtinfo6 (= 6.5-2), libtirpc-common (= 1.3.4+ds-1.3), libtirpc3t64 (= 1.3.4+ds-1.3), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-4), libubsan1 (= 14.2.0-4), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), media-types (= 10.1.0), mummer (= 3.23+dfsg-8), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), netbase (= 6.4), openjdk-21-jdk-headless (= 21.0.5~6ea-1), openjdk-21-jre-headless (= 21.0.5~6ea-1), openssl (= 3.3.2-1), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), po-debconf (= 1.0.21+nmu1), python3 (= 3.12.5-1+b1), python3-autocommand (= 2.2.2-3), python3-inflect (= 7.3.1-1), python3-iniconfig (= 1.1.1-2), python3-jaraco.context (= 6.0.0-1), python3-jaraco.functools (= 4.0.2-1), python3-minimal (= 3.12.5-1+b1), python3-more-itertools (= 10.4.0-1), python3-networkx (= 3.2.1-4), python3-numpy (= 1:1.26.4+ds-11), python3-packaging (= 24.1-1), python3-pkg-resources (= 74.1.2-2), python3-pluggy (= 1.5.0-1), python3-pysam (= 0.22.1+ds-2+b1), python3-pytest (= 8.3.2-1), python3-setuptools (= 74.1.2-2), python3-typeguard (= 4.3.0-1), python3-typing-extensions (= 4.12.2-2), python3-zipp (= 3.20.1-1), python3.12 (= 3.12.6-1), python3.12-minimal (= 3.12.6-1), readline-common (= 8.2-5), rpcsvc-proto (= 1.4.3-1), samtools (= 1.20-3), sed (= 4.9-2), sensible-utils (= 0.0.24), smalt (= 0.7.6-13), sysvinit-utils (= 3.10-2), tar (= 1.35+dfsg-3), tzdata (= 2024a-4), usr-is-merged (= 39), util-linux (= 2.40.2-8), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1706790897" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iva_1.0.11+ds-5_amd64.deb ------------------------- new Debian package, version 2.0. size 8581760 bytes: control archive=3012 bytes. 951 bytes, 21 lines control 5542 bytes, 65 lines md5sums 253 bytes, 12 lines * postinst #!/bin/sh 366 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.11+ds-5 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 8770 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 2024-02-01 12:34 ./ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/bin/ -rwxr-xr-x root/root 17240 2024-02-01 12:34 ./usr/bin/iva -rwxr-xr-x root/root 6228 2024-02-01 12:34 ./usr/bin/iva_qc -rwxr-xr-x root/root 2406 2024-02-01 12:34 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/ -rw-r--r-- root/root 602 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt -rw-r--r-- root/root 4 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2024-02-01 12:34 ./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 4121 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- 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+------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 37724 Build-Time: 17 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 27 Job: /srv/debomatic/incoming/iva_1.0.11+ds-5.dsc Machine Architecture: amd64 Package: iva Package-Time: 49 Source-Version: 1.0.11+ds-5 Space: 37724 Status: successful Version: 1.0.11+ds-5 -------------------------------------------------------------------------------- Finished at 2024-09-15T12:12:14Z Build needed 00:00:49, 37724k disk space