I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 11 10:16:02 +14 2024 I: pbuilder-time-stamp: 1733861762 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-6.dsc] I: copying [./iva_1.0.11+ds.orig.tar.xz] I: copying [./iva_1.0.11+ds-6.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Dec 4 21:04:58 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-6.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-6.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 dpkg-source: info: applying syntax-warning.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/394497/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 10 20:16 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/394497/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/394497/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=d6efe93321cf4f60a403a21b74504fce LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=394497 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.s6MKzOfL/pbuilderrc_3XsU --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.s6MKzOfL/b2 --logfile b2/build.log iva_1.0.11+ds-6.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/394497/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: arm64 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 ... 20083 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} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libpcsclite1{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1t64{a} libssl-dev{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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} mummer{a} netbase{a} openjdk-21-jdk-headless{a} openjdk-21-jre-headless{a} openssl{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{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-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-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, 129 newly installed, 0 to remove and 0 not upgraded. Need to get 189 MB of archives. After unpacking 628 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-1 [808 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-1 [1930 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-4 [256 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 17 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-1 [1905 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-1 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libdata-stag-perl all 0.14-3 [448 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get: 47 http://deb.debian.org/debian trixie/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libtest-deep-perl all 1.204-1 [52.9 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libalgorithm-diff-perl all 1.201-1 [43.3 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libtext-diff-perl all 1.45-2 [27.2 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libtest-differences-perl all 0.71-1 [17.9 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libsub-uplevel-perl all 0.2800-3 [14.0 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libtest-exception-perl all 0.43-3 [16.9 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libtest-warn-perl all 0.37-2 [14.5 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libtest-most-perl all 0.38-1 [25.1 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 bioperl all 1.7.8-1 [246 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 ca-certificates-java all 20240118 [11.6 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 66 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 java-common all 0.76 [6776 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.36-1 [102 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.106-1 [1292 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libpcsclite1 arm64 2.3.0-3 [55.1 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jre-headless arm64 21.0.5+11-1 [40.6 MB] Get: 81 http://deb.debian.org/debian trixie/main arm64 default-jre-headless arm64 2:1.21-76 [3192 B] Get: 82 http://deb.debian.org/debian trixie/main arm64 openjdk-21-jdk-headless arm64 21.0.5+11-1 [81.9 MB] Get: 83 http://deb.debian.org/debian trixie/main arm64 default-jdk-headless arm64 2:1.21-76 [1124 B] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 90 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 fastaq all 3.17.0-9 [47.8 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 kmc arm64 3.2.4+dfsg-1+b1 [889 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libbambamc0 arm64 0.0.50-6+b2 [34.6 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB] Fetched 189 MB in 1s (268 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 ... 20083 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-5) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (Reading database ... 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Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../13-libpython3.12-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.8-1_arm64.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../15-libpython3-stdlib_3.12.6-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21680 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_arm64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.2-2_arm64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... 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Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../018-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../019-libdata-stag-perl_0.14-3_all.deb ... Unpacking libdata-stag-perl (0.14-3) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../020-libbio-perl-perl_1.7.8-1_all.deb ... Unpacking libbio-perl-perl (1.7.8-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../021-libclass-data-inheritable-perl_0.10-1_all.deb ... Unpacking libclass-data-inheritable-perl (0.10-1) ... 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) ... Selecting previously unselected package libtext-diff-perl. Preparing to unpack .../027-libtext-diff-perl_1.45-2_all.deb ... Unpacking libtext-diff-perl (1.45-2) ... Selecting previously unselected package libtest-differences-perl. Preparing to unpack .../028-libtest-differences-perl_0.71-1_all.deb ... Unpacking libtest-differences-perl (0.71-1) ... Selecting previously unselected package libsub-uplevel-perl. Preparing to unpack .../029-libsub-uplevel-perl_0.2800-3_all.deb ... Unpacking libsub-uplevel-perl (0.2800-3) ... Selecting previously unselected package libtest-exception-perl. Preparing to unpack .../030-libtest-exception-perl_0.43-3_all.deb ... Unpacking libtest-exception-perl (0.43-3) ... Selecting previously unselected package libtest-warn-perl. Preparing to unpack .../031-libtest-warn-perl_0.37-2_all.deb ... Unpacking libtest-warn-perl (0.37-2) ... Selecting previously unselected package libtest-most-perl. Preparing to unpack .../032-libtest-most-perl_0.38-1_all.deb ... 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_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../036-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../039-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../040-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../041-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../042-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../043-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../044-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../045-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../046-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 .../047-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../048-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package java-common. Preparing to unpack .../049-java-common_0.76_all.deb ... Unpacking java-common (0.76) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../050-liblcms2-2_2.16-2_arm64.deb ... Unpacking liblcms2-2:arm64 (2.16-2) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 10 20:16:29 UTC 2024. Universal Time is now: Tue Dec 10 20:16:29 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:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libnspr4:arm64 (2:4.36-1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libncurses6:arm64 (6.5-2+b1) ... Setting up libbambamc0:arm64 (0.0.50-6+b2) ... Setting up libssl-dev:arm64 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up libpcsclite1:arm64 (2.3.0-3) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up mummer (3.23+dfsg-8+b1) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up openssl (3.3.2-2) ... Setting up kmc (3.2.4+dfsg-1+b1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13+b1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libnss3:arm64 (2:3.106-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... 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:arm64 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up openjdk-21-jre-headless:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:arm64 (8.11.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libhts3t64:arm64 (1.20+ds-2) ... Setting up bioperl (1.7.8-1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up samtools (1.20-3+b1) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-packaging (24.2-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.1+ds-2+b3) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up fastaq (3.17.0-9) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-networkx (3.2.1-5) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... 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-21-jdk-headless:arm64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-arm64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up default-jdk-headless (2:1.21-76) ... 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: user script /srv/workspace/pbuilder/394497/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/394497/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/iva-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iva_1.0.11+ds-6_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/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 83ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] [parsing completed 29ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 5ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] [parsing completed 15ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] [parsing completed 52ms] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.random/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.jfr/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-21-openjdk-arm64/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/constant/Constable.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/lang/constant/ConstantDesc.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/util/Iterator.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/SequencedCollection.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/function/IntFunction.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [wrote /build/reproducible-path/iva-1.0.11+ds/iva/gage/GetFastaStats$ContigAt.class] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/jdk/internal/javac/PreviewFeature.class] [loading /modules/java.base/jdk/internal/javac/PreviewFeature$Feature.class] [loading /modules/java.base/jdk/internal/javac/PreviewFeature$JEP.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /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 2328ms] Note: /build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. dh_auto_build -- I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva copying iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim creating /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_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_3.12_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_3.12_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_3.12_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_3.12_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_3.12_iva/build/iva/test_run_data running build_scripts creating build/scripts-3.12 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.12 copying and adjusting scripts/iva_qc -> build/scripts-3.12 copying and adjusting scripts/iva -> build/scripts-3.12 changing mode of build/scripts-3.12/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.12/iva_qc from 644 to 755 changing mode of build/scripts-3.12/iva from 644 to 755 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 3.12.8, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /build/reproducible-path/iva-1.0.11+ds plugins: typeguard-4.4.1 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 =============================== ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'locate_file', 'read_text'} __version__ = Distribution().from_name('pyfastaq').version 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, 2 warnings in 8.98s ======================== 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 /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage running build_scripts running install_lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reference.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim/adapters.fasta -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/main.ratt.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config.hiv -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt_correction.pm -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/start.ratt.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/embl2gff.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/ratt/genbank2embl.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Pair.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Translate.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$ToProtein.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.class -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/colsum.pl -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getCorrectnessStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getMummerStats.sh -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.java -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/__init__.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/assembly.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/common.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/contig_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/edge.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/egg_extract.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/graph.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kcount.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kmers.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/mummer.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/qc_external.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/read_trim.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/seed_processor.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/test_data_runner.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/external_progs.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/kraken.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva copying /build/reproducible-path/iva-1.0.11+ds/.pybuild/cpython3_3.12_iva/build/iva/mapping.py -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/assembly.py to assembly.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/common.py to common.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/contig.py to contig.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/contig_trim.py to contig_trim.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/edge.py to edge.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/egg_extract.py to egg_extract.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/graph.py to graph.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kcount.py to kcount.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kmers.py to kmers.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/mummer.py to mummer.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc.py to qc.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/qc_external.py to qc_external.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim.py to read_trim.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed.py to seed.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/seed_processor.py to seed_processor.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/external_progs.py to external_progs.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/kraken.py to kraken.cpython-312.pyc byte-compiling /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/dist-packages/iva/mapping.py to mapping.cpython-312.pyc running install_egg_info running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12/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-3.12/iva -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.12/iva_qc -> /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin copying build/scripts-3.12/iva_qc_make_db -> /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 to 755 changing mode of /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/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-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../iva_1.0.11+ds-6_arm64.buildinfo dpkg-genchanges --build=binary -O../iva_1.0.11+ds-6_arm64.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: user script /srv/workspace/pbuilder/394497/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/394497/tmp/hooks/B01_cleanup finished 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/394497 and its subdirectories I: Current time: Wed Dec 11 10:17:30 +14 2024 I: pbuilder-time-stamp: 1733861850