Sat May 11 08:19:35 UTC 2024 I: starting to build iva/trixie/amd64 on jenkins on '2024-05-11 08:19' Sat May 11 08:19:35 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/19516/console.log Sat May 11 08:19:35 UTC 2024 I: Downloading source for trixie/iva=1.0.11+ds-5 --2024-05-11 08:19:36-- http://deb.debian.org/debian/pool/main/i/iva/iva_1.0.11%2bds-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2289 (2.2K) [text/prs.lines.tag] Saving to: ‘iva_1.0.11+ds-5.dsc’ 0K .. 100% 337M=0s 2024-05-11 08:19:36 (337 MB/s) - ‘iva_1.0.11+ds-5.dsc’ saved [2289/2289] Sat May 11 08:19:36 UTC 2024 I: iva_1.0.11+ds-5.dsc -----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----- Sat May 11 08:19:36 UTC 2024 I: Checking whether the package is not for us Sat May 11 08:19:36 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sat May 11 08:19:36 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sat May 11 08:24:16 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 10 20:19:39 -12 2024 I: pbuilder-time-stamp: 1715415579 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.11+ds-5.dsc] I: copying [./iva_1.0.11+ds.orig.tar.xz] I: copying [./iva_1.0.11+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 1 12:52:13 2024 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 iva-1.0.11+ds 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1476552/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2066d6e408224d4499ecd327362ba15c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1476552' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/pbuilderrc_UBPt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/b1 --logfile b1/build.log iva_1.0.11+ds-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1476552/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on bioperl; however: Package bioperl is not installed. pbuilder-satisfydepends-dummy depends on fastaq; however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on kmc; however: Package kmc is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-packaging; however: Package python3-packaging is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on smalt; however: Package smalt is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-headless; however: Package default-jdk-headless is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bioperl{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jdk-headless{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} java-common{a} kmc{a} libalgorithm-diff-perl{a} libarchive-zip-perl{a} libbambamc0{a} libbio-perl-perl{a} libblas3{a} libbrotli1{a} libcapture-tiny-perl{a} libclass-data-inheritable-perl{a} libcom-err2{a} libcurl3t64-gnutls{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate0{a} libdevel-stacktrace-perl{a} libelf1t64{a} libexception-class-perl{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-string-perl{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsub-uplevel-perl{a} libtest-deep-perl{a} libtest-differences-perl{a} libtest-exception-perl{a} libtest-most-perl{a} libtest-warn-perl{a} libtext-diff-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} mummer{a} netbase{a} openjdk-17-jdk-headless{a} openjdk-17-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-distutils{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pysam{a} python3-pytest{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} smalt{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run curl krb5-locales libace-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libapache-dbi-perl libarchive-cpio-perl libarray-compare-perl libasound2t64 libbio-asn1-entrezgene-perl libbio-perl-run-perl libcache-cache-perl libclone-perl libconvert-binary-c-perl libcups2t64 libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libfontconfig1 libfreetype6 libgd-perl libgpm2 libgraph-perl libgraphviz-perl libharfbuzz0b libhtml-parser-perl libhtml-tableextract-perl libhttp-message-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libyaml-perl lynx perl-doc perl-tk publicsuffix python3-gdal python3-matplotlib python3-pydot python3-pygments python3-pygraphviz python3-scipy python3-yaml wget 0 packages upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 172 MB of archives. After unpacking 531 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 bioperl all 1.7.8-1 [246 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 58 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 java-common all 0.75 [6640 B] Get: 67 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libnspr4 amd64 2:4.35-1.1+b1 [109 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libnss3 amd64 2:3.99-1 [1408 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libpcsclite1 amd64 2.0.3-1 [51.0 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jre-headless amd64 17.0.11+9-1 [43.8 MB] Get: 73 http://deb.debian.org/debian trixie/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get: 74 http://deb.debian.org/debian trixie/main amd64 openjdk-17-jdk-headless amd64 17.0.11+9-1 [71.4 MB] Get: 75 http://deb.debian.org/debian trixie/main amd64 default-jdk-headless amd64 2:1.17-75 [1108 B] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 86 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 kmc amd64 3.2.4+dfsg-1 [1015 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 111 http://deb.debian.org/debian trixie/main amd64 python3-networkx all 2.8.8-2 [1425 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 smalt amd64 0.7.6-13 [115 kB] Fetched 172 MB in 6s (29.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libsigsegv2:amd64 (2.14-1+b1) ... Selecting previously unselected package gawk. (Reading database ... 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Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20260 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21220 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.2.1-3_amd64.deb ... Unpacking openssl (3.2.1-3) ... 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Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../022-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../023-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libtest-deep-perl. Preparing to unpack .../024-libtest-deep-perl_1.204-1_all.deb ... Unpacking libtest-deep-perl (1.204-1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../025-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libalgorithm-diff-perl. Preparing to unpack .../026-libalgorithm-diff-perl_1.201-1_all.deb ... Unpacking libalgorithm-diff-perl (1.201-1) ... 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Unpacking libtest-most-perl (0.38-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../033-bioperl_1.7.8-1_all.deb ... Unpacking bioperl (1.7.8-1) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../034-ca-certificates-java_20240118_all.deb ... Unpacking ca-certificates-java (20240118) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../035-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../036-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../037-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../038-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../039-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../040-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../041-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../042-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../043-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../044-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../045-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../046-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../047-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../048-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../049-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package java-common. Preparing to unpack .../050-java-common_0.75_all.deb ... Unpacking java-common (0.75) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../051-liblcms2-2_2.14-2+b1_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../052-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../053-libnspr4_2%3a4.35-1.1+b1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:amd64. Preparing to unpack .../054-libnss3_2%3a3.99-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.99-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../055-libpcsclite1_2.0.3-1_amd64.deb ... Unpacking libpcsclite1:amd64 (2.0.3-1) ... Selecting previously unselected package openjdk-17-jre-headless:amd64. Preparing to unpack .../056-openjdk-17-jre-headless_17.0.11+9-1_amd64.deb ... Unpacking openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../057-default-jre-headless_2%3a1.17-75_amd64.deb ... Unpacking default-jre-headless (2:1.17-75) ... Selecting previously unselected package openjdk-17-jdk-headless:amd64. Preparing to unpack .../058-openjdk-17-jdk-headless_17.0.11+9-1_amd64.deb ... Unpacking openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... Selecting previously unselected package default-jdk-headless. Preparing to unpack .../059-default-jdk-headless_2%3a1.17-75_amd64.deb ... Unpacking default-jdk-headless (2:1.17-75) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../060-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../061-python3-lib2to3_3.12.3-1_all.deb ... Unpacking python3-lib2to3 (3.12.3-1) ... 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Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up java-common (0.75) ... 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 libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sat May 11 08:22:04 UTC 2024. Universal Time is now: Sat May 11 08:22:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. 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 (6.4+20240414-1) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up libssl-dev:amd64 (3.2.1-3) ... Setting up autopoint (0.21-14) ... Setting up libpcsclite1:amd64 (2.0.3-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... 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 (0.0.22) ... 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 libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up openssl (3.2.1-3) ... Setting up kmc (3.2.4+dfsg-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... 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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnss3:amd64 (2:3.99-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-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 (1.20.1-6+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up python3 (3.11.8-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-packaging (24.0-1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up bioperl (1.7.8-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (7.4.4-3) ... Setting up debhelper (13.15.3) ... Setting up python3-networkx (2.8.8-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up python3-numpy (1:1.26.4+ds-8) ... Setting up dh-python (6.20240422) ... Setting up fastaq (3.17.0-6) ... Processing triggers for libc-bin (2.38-7) ... 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:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian: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:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian: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: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: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:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian: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:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_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:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.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:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:amd64 (17.0.11+9-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up default-jdk-headless (2:1.17-75) ... 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. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/iva-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iva_1.0.11+ds-5_source.changes 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 --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 '/build/reproducible-path/iva-1.0.11+ds' rm -rf .pybuild *.egg-info .pytest_cache build rm -f iva/gage/*.class rm -rf /build/reproducible-path/iva-1.0.11+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild 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: python3.11 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds' chmod a-x /build/reproducible-path/iva-1.0.11+ds/iva/read_trim/adapters.fasta chmod a+x /build/reproducible-path/iva-1.0.11+ds/iva/gage/getCorrectnessStats.sh chmod a+x /build/reproducible-path/iva-1.0.11+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /build/reproducible-path/iva-1.0.11+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.java]] [parsing completed 257ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] [parsing completed 33ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 18ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] [parsing completed 74ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] [parsing completed 33ms] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.random/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.incubator.foreign/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.sctp/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-17-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/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/util/Iterator.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/util/Optional.class] [loading /modules/java.base/java/lang/Enum$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$OfField.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$Pair.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$Translate.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils$ToProtein.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.class] [total 4203ms] dh_auto_build -- I: pybuild base:311: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva copying iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.11 copying and adjusting scripts/iva -> build/scripts-3.11 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.11 copying and adjusting scripts/iva_qc -> build/scripts-3.11 changing mode of build/scripts-3.11/iva from 644 to 755 changing mode of build/scripts-3.11/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.11/iva_qc from 644 to 755 make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds' python3 -m pytest --verbose ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/iva-1.0.11+ds 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 /build/reproducible-path/iva-1.0.11+ds/iva/mapping.py:161: DeprecationWarning: 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 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /build/reproducible-path/iva-1.0.11+ds/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 24.54s ======================= make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' 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 /build/reproducible-path/iva-1.0.11+ds/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install /usr/lib/python3/dist-packages/setuptools/_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 running build_scripts running install_lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11 creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mapping.py to mapping.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/egg_extract.py to egg_extract.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed.py to seed.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim.py to read_trim.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/graph.py to graph.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/assembly.py to assembly.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/edge.py to edge.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc_external.py to qc_external.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig.py to contig.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/common.py to common.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/external_progs.py to external_progs.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc.py to qc.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed_processor.py to seed_processor.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kcount.py to kcount.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig_trim.py to contig_trim.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kraken.py to kraken.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kmers.py to kmers.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mummer.py to mummer.cpython-311.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-311.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 /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.11/iva -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.11/iva_qc_make_db -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.11/iva_qc -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva to 755 changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/iva-1.0.11+ds' mkdir -p /build/reproducible-path/iva-1.0.11+ds/debian/man PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /build/reproducible-path/iva-1.0.11+ds/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 '/build/reproducible-path/iva-1.0.11+ds' 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 --build=binary -O../iva_1.0.11+ds-5_amd64.buildinfo dpkg-genchanges --build=binary -O../iva_1.0.11+ds-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1476552 and its subdirectories I: Current time: Fri May 10 20:24:15 -12 2024 I: pbuilder-time-stamp: 1715415855 Sat May 11 08:24:17 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Sat May 11 08:24:17 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Sat May 11 08:25:36 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Sat May 11 08:25:37 UTC 2024 I: 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: amd64 Version: 1.0.11+ds-5 Distribution: unstable 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. Checksums-Sha1: 412cc0ecff1b070b82f08856943a8b20989a96d8 7767 iva_1.0.11+ds-5_amd64.buildinfo 663b8b9c82c5763e4dbf064ead9643257bca04bc 8581624 iva_1.0.11+ds-5_amd64.deb Checksums-Sha256: d8873bcdf69808f5761baf8490b7bde5c0e60d3c91ea2c28907c1c9aab575ad3 7767 iva_1.0.11+ds-5_amd64.buildinfo 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef 8581624 iva_1.0.11+ds-5_amd64.deb Files: e9f6bc28a96a63244a762fcc5678efa1 7767 science optional iva_1.0.11+ds-5_amd64.buildinfo 81641314ba9e9e3b5e100a7443802397 8581624 science optional iva_1.0.11+ds-5_amd64.deb Sat May 11 08:25:38 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_23-19516.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/iva_1.0.11+ds-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/iva_1.0.11+ds-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/iva_1.0.11+ds-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/b1/iva_1.0.11+ds-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.42awaPle/b2/iva_1.0.11+ds-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.545s) 0.544s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.115s) 0.115s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 941ms CPU time consumed: 942ms Sat May 11 08:25:40 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat May 11 08:25:40 UTC 2024 I: iva from trixie built successfully and reproducibly on amd64. Sat May 11 08:25:41 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 11 08:25:41 UTC 2024 I: Submitting 12K b1/iva_1.0.11+ds-5_amd64.buildinfo.asc Sat May 11 08:25:42 UTC 2024 I: Submitting 12K b2/iva_1.0.11+ds-5_amd64.buildinfo.asc Sat May 11 08:25:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 11 08:25:43 UTC 2024 I: Done submitting .buildinfo files. Sat May 11 08:25:43 UTC 2024 I: Removing signed iva_1.0.11+ds-5_amd64.buildinfo.asc files: removed './b1/iva_1.0.11+ds-5_amd64.buildinfo.asc' removed './b2/iva_1.0.11+ds-5_amd64.buildinfo.asc'