Running as unit: rb-build-arm64_11-71673.service ==================================================================================== Wed Nov 20 23:59:07 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_11) on jenkins, called using "codethink03-arm64 codethink04-arm64" as arguments. Wed Nov 20 23:59:07 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-FKIZvNV5" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Nov 20 23:59:08 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Nov 20 23:59:08 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-CQ1SPQ' Wed Nov 20 23:59:08 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Wed Nov 20 23:59:08 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-bfwdKj' ok, let's check if iva is building anywhere yet… ok, iva is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of iva in trixie on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink04-arm64.debian.net. ============================================================================= Wed Nov 20 23:59:31 UTC 2024 I: starting to build iva/trixie/arm64 on jenkins on '2024-11-20 23:59' Wed Nov 20 23:59:31 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_11/71673/console.log 1732147171 arm64 trixie iva Wed Nov 20 23:59:31 UTC 2024 I: Downloading source for trixie/iva=1.0.11+ds-5 --2024-11-20 23:59:32-- http://deb.debian.org/debian/pool/main/i/iva/iva_1.0.11%2bds-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2289 (2.2K) [text/prs.lines.tag] Saving to: ‘iva_1.0.11+ds-5.dsc’ 0K .. 100% 323M=0s 2024-11-20 23:59:32 (323 MB/s) - ‘iva_1.0.11+ds-5.dsc’ saved [2289/2289] --2024-11-20 23:59:32-- http://deb.debian.org/debian/pool/main/i/iva/iva_1.0.11%2bds-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2289 (2.2K) [text/prs.lines.tag] Saving to: ‘iva_1.0.11+ds-5.dsc’ 0K .. 100% 323M=0s 2024-11-20 23:59:32 (323 MB/s) - ‘iva_1.0.11+ds-5.dsc’ saved [2289/2289] Wed Nov 20 23:59:32 UTC 2024 I: iva_1.0.11+ds-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.11+ds-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Testsuite: autopkgtest Testsuite-Triggers: python3-packaging, trimmomatic Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libssl-dev, bioperl, fastaq, kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless Package-List: iva deb science optional arch=any Checksums-Sha1: f333165445174c86c83460fe990b625f7ae3aff5 8680588 iva_1.0.11+ds.orig.tar.xz 30c67565ccddfecdcac0a5e1fe6da1278ef3481c 5992 iva_1.0.11+ds-5.debian.tar.xz Checksums-Sha256: 0835a11746deaa4067aeb1bc9817ed8d415f36de51ae4fc122ea5b287c5ecf1d 8680588 iva_1.0.11+ds.orig.tar.xz aea1686cc3a60ec0fbfd9340b5332cf0430cd814f96ae1ac6992cb8e6f8a6467 5992 iva_1.0.11+ds-5.debian.tar.xz Files: e7b6c8d9cc2adb23b0d90168122c33b3 8680588 iva_1.0.11+ds.orig.tar.xz 0ef1450aea819feff2cd1b7b0edb906a 5992 iva_1.0.11+ds-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW7k/0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEx8g/9GbdcWmPxrT733yvQimaZFg00Iy6yqAmj +K7oOvPXC4nkJ5Ft/5KR8bRueC3DIPLL5VmrttD14SICFi0Be8VcP8I4I7TOQi0z xkiC80VAIUSKJ9GDo+jMRWkB93bFnsnuCILAgC2b6eIfWeyGB4xX+qv/qqNpaY+s lIoHTpRXnIaWGWcxJfs132HoJeeUjWuqrt7UG7apx61aB0P3imVpZYFbvyvROuN5 zxnj0ga+hw/pqBikfRQCnQu1Me3aMOurE7Q42N2CSO8A2VCFzCX3DYGhRCFKZuE0 cTOxmwO88ZUN80fAbm7mTMOrQpwMFsMtbVEIHk6o8hx8IiUn43gbf1pMRaKLhKK8 BMncd8ME+zVpI8F/Ag5209h1Eawibwd+dM4J+cHN2ENe4M1P3Qc2bw4a5vhi2+H/ p0mhCyYpNG2XU0VnnoNhpCU5dLrX7mYaEbjR19y9A98kCFFqSQ6yJmIyC8icm5HI 9SVS0U6tU6qbC1jmhqI313VlYYN+qH5t1z71ktLo4Uq5khmdC/Qrv2XVhARkS+Tr ZmOMQGJIwgC0hkKFpuNtzcocTIlAQSyo7QQCPVsNYh//UCyk1RPO9Ta1LpsNQ0hN Q33gwdEqgMMrZW30A9qyR71bno5aRznYe8FeNt/razi5XHm5U2eipEcmwCEU4jN5 0Eq06ewO6c0= =RITE -----END PGP SIGNATURE----- Wed Nov 20 23:59:32 UTC 2024 I: Checking whether the package is not for us Wed Nov 20 23:59:32 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Wed Nov 20 23:59:32 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Wed Nov 20 23:59:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Wed Nov 20 23:59:32 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Mn6NpI' ==================================================================================== Tue Jan 26 12:45:33 UTC 2027 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 iva trixie /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf 1.0.11+ds-5" as arguments. Tue Jan 26 12:45:33 UTC 2027 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-GN696xku" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Jan 26 12:45:33 UTC 2027 I: Downloading source for trixie/iva=1.0.11+ds-5 Reading package lists... NOTICE: 'iva' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iva.git Please use: git clone https://salsa.debian.org/med-team/iva.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8689 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (dsc) [2289 B] Get:2 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (tar) [8681 kB] Get:3 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (diff) [5992 B] Fetched 8689 kB in 1s (17.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'iva' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iva.git Please use: git clone https://salsa.debian.org/med-team/iva.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8689 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (dsc) [2289 B] Get:2 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (tar) [8681 kB] Get:3 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (diff) [5992 B] Fetched 8689 kB in 1s (17.3 MB/s) Download complete and in download only mode ============================================================================= Building iva in trixie on arm64 on codethink03-arm64 now. Date: Tue Jan 26 12:45:34 GMT 2027 Date UTC: Tue Jan 26 12:45:34 UTC 2027 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 26 00:45:34 -12 2027 I: pbuilder-time-stamp: 1800967534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.11+ds-5.dsc] I: copying [./iva_1.0.11+ds.orig.tar.xz] I: copying [./iva_1.0.11+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 1 12:52:13 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting iva in iva-1.0.11+ds dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.11+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1352670/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='a5c8c1625ad94e658ef96f3c8bc885db' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1352670' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/pbuilderrc_DZo7 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1 --logfile b1/build.log iva_1.0.11+ds-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1352670/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 ... 20087 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-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: 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 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, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 190 MB of archives. After unpacking 622 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 3.12.7-3 [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 3.12.7-3 [1940 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-3 [255 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 1.47.1-1+b1 [23.1 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 3.12.7-3 [1902 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.7-3 [671 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 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 2:4.35-1.1+b1 [101 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.105-2 [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 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 fastaq all 3.17.0-8 [47.7 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 kmc arm64 3.2.4+dfsg-1+b1 [889 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libbambamc0 arm64 0.0.50-6+b2 [34.6 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB] Fetched 190 MB in 1s (142 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 ... 20087 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 ... (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 ... 20129 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_arm64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:arm64 (3.12.7-3) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20653 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... 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_3.12.7-3_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.7-3_arm64.deb ... Unpacking python3.12 (3.12.7-3) ... 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 ... 21683 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) ... 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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 (1.47.1-1+b1) ... 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-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 26 12:46:25 UTC 2027. Universal Time is now: Tue Jan 26 12:46:25 UTC 2027. 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 (3.12.0-3+b1) ... 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 (2:4.35-1.1+b1) ... 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 (1.4.0-1+b1) ... 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 (1.6.0-1) ... 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 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13+b1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... 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 (2:3.105-2) ... 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 (1.23.0-5) ... 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 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... 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 (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... 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 (3.17.0-8) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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: Running cd /build/reproducible-path/iva-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iva_1.0.11+ds-5_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 131ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] [parsing completed 25ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] [parsing completed 49ms] [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 2781ms] 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/external_progs.py -> /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/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/kraken.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 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 3.12.7, 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 =============================== iva/mapping.py:161 /build/reproducible-path/iva-1.0.11+ds/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) ../../../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/external_progs.py:33 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /build/reproducible-path/iva-1.0.11+ds/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ====================== 160 passed, 10 warnings in 12.69s ======================= 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 creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12 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/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/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/mapping.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 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/kraken.py to kraken.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' byte-compiling /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/mapping.py to mapping.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' 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 /usr/lib/python3.12/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 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-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../iva_1.0.11+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../iva_1.0.11+ds-5_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: 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/1352670 and its subdirectories I: Current time: Tue Jan 26 00:47:54 -12 2027 I: pbuilder-time-stamp: 1800967674 Tue Jan 26 12:47:54 UTC 2027 I: Signing ./b1/iva_1.0.11+ds-5_arm64.buildinfo as iva_1.0.11+ds-5_arm64.buildinfo.asc Tue Jan 26 12:47:54 UTC 2027 I: Signed ./b1/iva_1.0.11+ds-5_arm64.buildinfo as ./b1/iva_1.0.11+ds-5_arm64.buildinfo.asc Tue Jan 26 12:47:54 UTC 2027 - build #1 for iva/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Tue Jan 26 12:47:54 UTC 2027 - reproducible_build.sh stopped running as /tmp/jenkins-script-GN696xku, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:01 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 20 23:59 b2 -rw-r--r-- 1 jenkins jenkins 2289 Feb 1 2024 iva_1.0.11+ds-5.dsc -rw------- 1 jenkins jenkins 3389 Nov 20 23:59 rbuildlog.AxYqyaP /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1: total 8548 -rw-r--r-- 1 jenkins jenkins 123478 Nov 21 00:01 build.log -rw-r--r-- 1 jenkins jenkins 5992 Nov 21 00:01 iva_1.0.11+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:01 iva_1.0.11+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 7983 Nov 21 00:01 iva_1.0.11+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8865 Nov 21 00:01 iva_1.0.11+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1220 Nov 21 00:01 iva_1.0.11+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 8581760 Nov 21 00:01 iva_1.0.11+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1384 Nov 21 00:01 iva_1.0.11+ds-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b2: total 0 Thu Nov 21 00:01:55 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 26 00:45:34 -12 2027 I: pbuilder-time-stamp: 1800967534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.11+ds-5.dsc] I: copying [./iva_1.0.11+ds.orig.tar.xz] I: copying [./iva_1.0.11+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 1 12:52:13 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting iva in iva-1.0.11+ds dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.11+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1352670/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='a5c8c1625ad94e658ef96f3c8bc885db' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1352670' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/pbuilderrc_DZo7 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1 --logfile b1/build.log iva_1.0.11+ds-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1352670/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 ... 20087 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-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: 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 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, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 190 MB of archives. After unpacking 622 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 3.12.7-3 [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 3.12.7-3 [1940 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-3 [255 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 1.47.1-1+b1 [23.1 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 3.12.7-3 [1902 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.7-3 [671 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 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 2:4.35-1.1+b1 [101 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.105-2 [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 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 fastaq all 3.17.0-8 [47.7 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 kmc arm64 3.2.4+dfsg-1+b1 [889 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libbambamc0 arm64 0.0.50-6+b2 [34.6 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB] Fetched 190 MB in 1s (142 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 ... 20087 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) ... 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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) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../051-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../052-libnspr4_2%3a4.35-1.1+b1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../053-libnss3_2%3a3.105-2_arm64.deb ... Unpacking libnss3:arm64 (2:3.105-2) ... Selecting previously unselected package libpcsclite1:arm64. Preparing to unpack .../054-libpcsclite1_2.3.0-3_arm64.deb ... Unpacking libpcsclite1:arm64 (2.3.0-3) ... Selecting previously unselected package openjdk-21-jre-headless:arm64. Preparing to unpack .../055-openjdk-21-jre-headless_21.0.5+11-1_arm64.deb ... Unpacking openjdk-21-jre-headless:arm64 (21.0.5+11-1) ... Selecting previously unselected package default-jre-headless. 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Unpacking libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../078-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../079-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../080-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../081-libcurl3t64-gnutls_8.11.0-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.11.0-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../082-libdeflate0_1.22-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.22-1) ... 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Preparing to unpack .../101-python3-pysam_0.22.1+ds-2+b3_arm64.deb ... Unpacking python3-pysam (0.22.1+ds-2+b3) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../102-python3-pytest_8.3.3-1_all.deb ... Unpacking python3-pytest (8.3.3-1) ... Selecting previously unselected package smalt. Preparing to unpack .../103-smalt_0.7.6-13+b1_arm64.deb ... Unpacking smalt (0.7.6-13+b1) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up java-common (0.76) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up gawk (1:5.2.1-2+b2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1: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 (1.47.1-1+b1) ... 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-3) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 26 12:46:25 UTC 2027. Universal Time is now: Tue Jan 26 12:46:25 UTC 2027. 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 (3.12.0-3+b1) ... 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 (2:4.35-1.1+b1) ... 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 (1.4.0-1+b1) ... 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 (1.6.0-1) ... 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 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13+b1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... 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 (2:3.105-2) ... 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 (1.23.0-5) ... 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 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... 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 (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... 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 (3.17.0-8) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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: Running cd /build/reproducible-path/iva-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iva_1.0.11+ds-5_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 131ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] [parsing completed 25ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] [parsing completed 49ms] [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 2781ms] 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/external_progs.py -> /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/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/kraken.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 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 3.12.7, 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 =============================== iva/mapping.py:161 /build/reproducible-path/iva-1.0.11+ds/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) ../../../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/external_progs.py:33 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /build/reproducible-path/iva-1.0.11+ds/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ====================== 160 passed, 10 warnings in 12.69s ======================= 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 creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12 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/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/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/mapping.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 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/kraken.py to kraken.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' byte-compiling /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/mapping.py to mapping.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' 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 /usr/lib/python3.12/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 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-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../iva_1.0.11+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../iva_1.0.11+ds-5_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: 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/1352670 and its subdirectories I: Current time: Tue Jan 26 00:47:54 -12 2027 I: pbuilder-time-stamp: 1800967674 Thu Nov 21 00:01:56 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Thu Nov 21 00:01:56 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Thu Nov 21 00:01:56 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Thu Nov 21 00:01:56 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-DlNAih' ==================================================================================== Thu Nov 21 00:01:58 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "2 iva trixie /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf 1.0.11+ds-5" as arguments. Thu Nov 21 00:01:58 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-aFerC6wk" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 00:01:58 UTC 2024 I: Downloading source for trixie/iva=1.0.11+ds-5 Reading package lists... NOTICE: 'iva' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iva.git Please use: git clone https://salsa.debian.org/med-team/iva.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8689 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (dsc) [2289 B] Get:2 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (tar) [8681 kB] Get:3 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (diff) [5992 B] Fetched 8689 kB in 0s (92.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'iva' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iva.git Please use: git clone https://salsa.debian.org/med-team/iva.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8689 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (dsc) [2289 B] Get:2 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (tar) [8681 kB] Get:3 http://deb.debian.org/debian trixie/main iva 1.0.11+ds-5 (diff) [5992 B] Fetched 8689 kB in 0s (92.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building iva in trixie on arm64 on codethink04-arm64 now. Date: Thu Nov 21 00:01:58 GMT 2024 Date UTC: Thu Nov 21 00:01:58 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/pbuilderrc_DJe6 + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' iva = debian-installer -o iva = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' iva = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.bxq6Socf/pbuilderrc_DJe6 --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.bxq6Socf/b2 --logfile b2/build.log iva_1.0.11+ds-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 21 14:01:58 +14 2024 I: pbuilder-time-stamp: 1732147318 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iva_1.0.11+ds-5.dsc] I: copying [./iva_1.0.11+ds.orig.tar.xz] I: copying [./iva_1.0.11+ds-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Feb 1 12:52:13 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting iva in iva-1.0.11+ds dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.11+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/929175/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-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 Nov 21 00:02 /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/929175/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/929175/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(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=a7680f666b3941eea35b6cfe6f05b4ff 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=929175 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.bxq6Socf/pbuilderrc_DJe6 --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.bxq6Socf/b2 --logfile b2/build.log iva_1.0.11+ds-5.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 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/929175/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 ... 20087 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-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: 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 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, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 190 MB of archives. After unpacking 622 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 3.12.7-3 [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 3.12.7-3 [1940 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-3 [255 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 1.47.1-1+b1 [23.1 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 3.12.7-3 [1902 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.7-3 [671 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 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 2:4.35-1.1+b1 [101 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.105-2 [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 74.1.2-2 [213 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.20-3+b1 [629 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 fastaq all 3.17.0-8 [47.7 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 kmc arm64 3.2.4+dfsg-1+b1 [889 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libbambamc0 arm64 0.0.50-6+b2 [34.6 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-3+b1 [98.9 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3+b1 [1812 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB] Fetched 190 MB in 1s (248 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 ... 20087 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 ... (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 ... 20129 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.12-minimal:arm64. 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Preparing to unpack .../101-python3-pysam_0.22.1+ds-2+b3_arm64.deb ... Unpacking python3-pysam (0.22.1+ds-2+b3) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../102-python3-pytest_8.3.3-1_all.deb ... Unpacking python3-pytest (8.3.3-1) ... Selecting previously unselected package smalt. Preparing to unpack .../103-smalt_0.7.6-13+b1_arm64.deb ... Unpacking smalt (0.7.6-13+b1) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up java-common (0.76) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up gawk (1:5.2.1-2+b2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1: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 (1.47.1-1+b1) ... 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-3) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 21 00:02:25 UTC 2024. Universal Time is now: Thu Nov 21 00:02:25 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 (3.12.0-3+b1) ... 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 (2:4.35-1.1+b1) ... 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 (1.4.0-1+b1) ... 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 (1.6.0-1) ... 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 (1.6.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up smalt (0.7.6-13+b1) ... Setting up liblapack3:arm64 (3.12.0-3+b1) ... 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 (2:3.105-2) ... 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 (1.23.0-5) ... 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 (3.12.7-3) ... Setting up python3.12 (3.12.7-3) ... 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 (24.1-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-more-itertools (10.5.0-1) ... 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 (3.17.0-8) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-typeguard (4.4.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-3) ... 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/929175/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/929175/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-5_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 46ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] [parsing completed 5ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] [parsing completed 11ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] [parsing completed 16ms] [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 1230ms] 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/external_progs.py -> /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/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/kraken.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 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 3.12.7, 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 =============================== iva/mapping.py:161 /build/reproducible-path/iva-1.0.11+ds/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'} __version__ = Distribution().from_name('pyfastaq').version iva/external_progs.py:33 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /build/reproducible-path/iva-1.0.11+ds/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /build/reproducible-path/iva-1.0.11+ds/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /build/reproducible-path/iva-1.0.11+ds/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 160 passed, 10 warnings in 5.42s ======================= 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 creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib creating /build/reproducible-path/iva-1.0.11+ds/debian/iva/usr/lib/python3.12 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/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/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/mapping.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 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/kraken.py to kraken.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' byte-compiling /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/mapping.py to mapping.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' 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 /usr/lib/python3.12/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 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-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../iva_1.0.11+ds-5_arm64.buildinfo dpkg-genchanges --build=binary -O../iva_1.0.11+ds-5_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/929175/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/929175/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/929175 and its subdirectories I: Current time: Thu Nov 21 14:03:09 +14 2024 I: pbuilder-time-stamp: 1732147389 + false + set +x Thu Nov 21 00:03:09 UTC 2024 I: Signing ./b2/iva_1.0.11+ds-5_arm64.buildinfo as iva_1.0.11+ds-5_arm64.buildinfo.asc Thu Nov 21 00:03:09 UTC 2024 I: Signed ./b2/iva_1.0.11+ds-5_arm64.buildinfo as ./b2/iva_1.0.11+ds-5_arm64.buildinfo.asc Thu Nov 21 00:03:09 UTC 2024 - build #2 for iva/trixie/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Thu Nov 21 00:03:09 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-aFerC6wk, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf: total 144 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:01 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 00:03 b2 -rw-r--r-- 1 jenkins jenkins 2289 Feb 1 2024 iva_1.0.11+ds-5.dsc -rw------- 1 jenkins jenkins 127168 Nov 21 00:01 rbuildlog.AxYqyaP /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1: total 8568 -rw-r--r-- 1 jenkins jenkins 123478 Nov 21 00:01 build.log -rw-r--r-- 1 jenkins jenkins 5992 Nov 21 00:01 iva_1.0.11+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:01 iva_1.0.11+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 7983 Nov 21 00:01 iva_1.0.11+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8865 Nov 21 00:01 iva_1.0.11+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1220 Nov 21 00:01 iva_1.0.11+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 8581760 Nov 21 00:01 iva_1.0.11+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1384 Nov 21 00:01 iva_1.0.11+ds-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b2: total 8548 -rw-r--r-- 1 jenkins jenkins 125410 Nov 21 00:03 build.log -rw-r--r-- 1 jenkins jenkins 5992 Nov 21 00:03 iva_1.0.11+ds-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2289 Nov 21 00:03 iva_1.0.11+ds-5.dsc -rw-r--r-- 1 jenkins jenkins 7983 Nov 21 00:03 iva_1.0.11+ds-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8865 Nov 21 00:03 iva_1.0.11+ds-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1220 Nov 21 00:03 iva_1.0.11+ds-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 8581760 Nov 21 00:03 iva_1.0.11+ds-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1384 Nov 21 00:03 iva_1.0.11+ds-5_source.changes Thu Nov 21 00:03:14 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Thu Nov 21 00:03:15 UTC 2024 I: iva_1.0.11+ds-5_arm64.changes: Format: 1.8 Date: Thu, 01 Feb 2024 13:34:57 +0100 Source: iva Binary: iva Architecture: arm64 Version: 1.0.11+ds-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: iva - iterative virus sequence assembler Closes: 1061804 Changes: iva (1.0.11+ds-5) unstable; urgency=medium . * Python3.12 compatibility by avoiding usage of distutils Closes: #1061804 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Remove patch reduce-ram.patch that is missing from debian/patches/series. Checksums-Sha1: fcba073cbb3a077f0ca08c2bdf3627fbca535cd4 7983 iva_1.0.11+ds-5_arm64.buildinfo a44e0071fdfd77f426102c139994cb2075c44610 8581760 iva_1.0.11+ds-5_arm64.deb Checksums-Sha256: 42eb6062fc531c275cc2383e15995f6094f996cc5da47d98f59cdd7509435149 7983 iva_1.0.11+ds-5_arm64.buildinfo 1ee6f44aec0ae5915863fd8aade19789860fe0a27a37e34a52cc4f770cb407bb 8581760 iva_1.0.11+ds-5_arm64.deb Files: 1cf5118d7586082a3b8dd3833ca132f2 7983 science optional iva_1.0.11+ds-5_arm64.buildinfo 7689810816dcab44984bbb26f9848b94 8581760 science optional iva_1.0.11+ds-5_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/iva_1.0.11+ds-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/iva_1.0.11+ds-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/iva_1.0.11+ds-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/iva_1.0.11+ds-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/iva_1.0.11+ds-5_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/iva_1.0.11+ds-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 00:01:55.166349343 +0000 +++ b2/build.log 2024-11-21 00:03:10.602937818 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 26 00:45:34 -12 2027 -I: pbuilder-time-stamp: 1800967534 +I: Current time: Thu Nov 21 14:01:58 +14 2024 +I: pbuilder-time-stamp: 1732147318 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1352670/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/929175/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Nov 21 00:02 /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/929175/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/929175/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(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 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + 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='a5c8c1625ad94e658ef96f3c8bc885db' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1352670' - PS1='# ' - PS2='> ' + INVOCATION_ID=a7680f666b3941eea35b6cfe6f05b4ff + 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=929175 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/pbuilderrc_DZo7 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1 --logfile b1/build.log iva_1.0.11+ds-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.bxq6Socf/pbuilderrc_DJe6 --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.bxq6Socf/b2 --logfile b2/build.log iva_1.0.11+ds-5.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 codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1352670/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/929175/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -275,7 +307,7 @@ Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.1+ds-2+b3 [3903 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB] -Fetched 190 MB in 1s (142 MB/s) +Fetched 190 MB in 1s (248 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 ... 20087 files and directories currently installed.) @@ -708,8 +740,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 26 12:46:25 UTC 2027. -Universal Time is now: Tue Jan 26 12:46:25 UTC 2027. +Local time is now: Thu Nov 21 00:02:25 UTC 2024. +Universal Time is now: Thu Nov 21 00:02:25 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libio-string-perl (1.08-4) ... @@ -1010,7 +1042,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/iva-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iva_1.0.11+ds-5_source.changes +I: user script /srv/workspace/pbuilder/929175/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/929175/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-5_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable @@ -1055,15 +1091,15 @@ 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 131ms] +[parsing completed 46ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SizeFasta.java]] -[parsing completed 4ms] +[parsing completed 5ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/Utils.java]] -[parsing completed 25ms] +[parsing completed 11ms] [parsing started SimpleFileObject[/build/reproducible-path/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]] -[parsing completed 49ms] +[parsing completed 16ms] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/java.xml/module-info.class] @@ -1247,7 +1283,7 @@ [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 2781ms] +[total 1230ms] 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 -- @@ -1510,7 +1546,7 @@ s = re.sub('\^.', '', s) ../../../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'} + /usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning: Unimplemented abstract methods {'read_text', 'locate_file'} __version__ = Distribution().from_name('pyfastaq').version iva/external_progs.py:33 @@ -1546,7 +1582,7 @@ class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -====================== 160 passed, 10 warnings in 12.69s ======================= +======================= 160 passed, 10 warnings in 5.42s ======================= make[1]: Leaving directory '/build/reproducible-path/iva-1.0.11+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1744,12 +1780,14 @@ 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/929175/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/929175/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/1352670 and its subdirectories -I: Current time: Tue Jan 26 00:47:54 -12 2027 -I: pbuilder-time-stamp: 1800967674 +I: removing directory /srv/workspace/pbuilder/929175 and its subdirectories +I: Current time: Thu Nov 21 14:03:09 +14 2024 +I: pbuilder-time-stamp: 1732147389 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/iva_1.0.11+ds-5.diff: 67.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/iva_1.0.11+ds-5.diff.gz b2/build.log: 84.1% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.5% -- replaced with stdout Thu Nov 21 00:03:16 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_iva_trixie_arm64_1732147396 + touch /var/log/reproducible-builds/diffoscope_stamp_iva_trixie_arm64_1732147396 + RESULT=0 + systemd-run '--description=diffoscope on iva/1.0.11+ds-5 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_11-71673 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf --run-session -c jenkins-reproducible-trixie-diffoscope-f5e663ac-03bb-4db5-9b81-752e108d3b31 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/dbd-tmp-pHvGUnR ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1/iva_1.0.11+ds-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b2/iva_1.0.11+ds-5_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_11-71673.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/iva_1.0.11+ds-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b1/iva_1.0.11+ds-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bxq6Socf/b2/iva_1.0.11+ds-5_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.399s) 0.399s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.087s) 0.087s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 746ms CPU time consumed: 698ms _ (_)_ ____ _ | \ \ / / _` | | |\ V / (_| | |_| \_/ \__,_| Thu Nov 21 00:03:18 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 00:03:18 UTC 2024 I: iva from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 00:03:19] INFO: Starting at 2024-11-21 00:03:19.482039 [2024-11-21 00:03:19] INFO: Generating the pages of 1 package(s) [2024-11-21 00:03:20] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/iva didn't produce a buildlog, even though it has been built. [2024-11-21 00:03:20] INFO: Finished at 2024-11-21 00:03:20.401064, took: 0:00:00.919032 Thu Nov 21 00:03:20 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/iva.html Thu Nov 21 00:03:20 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 00:03:20 UTC 2024 I: Submitting 12K b1/iva_1.0.11+ds-5_arm64.buildinfo.asc https://buildinfo.debian.net/fcba073cbb3a077f0ca08c2bdf3627fbca535cd4/iva_1.0.11+ds-5_arm64 Thu Nov 21 00:03:21 UTC 2024 I: Submitting 12K b2/iva_1.0.11+ds-5_arm64.buildinfo.asc https://buildinfo.debian.net/a6bb1d4e217080120c902c363e1147bd9c6461da/iva_1.0.11+ds-5_arm64 Thu Nov 21 00:03:22 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 00:03:22 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 00:03:22 UTC 2024 I: Removing signed iva_1.0.11+ds-5_arm64.buildinfo.asc files: removed './b1/iva_1.0.11+ds-5_arm64.buildinfo.asc' removed './b2/iva_1.0.11+ds-5_arm64.buildinfo.asc' 1732147402 arm64 trixie iva Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/iva_1.0.11+ds-5.rbuild.log: 82.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/iva_1.0.11+ds-5.rbuild.log.gz [2024-11-21 00:03:22] INFO: Starting at 2024-11-21 00:03:22.913036 [2024-11-21 00:03:22] INFO: Generating the pages of 1 package(s) [2024-11-21 00:03:23] INFO: Finished at 2024-11-21 00:03:23.815747, took: 0:00:00.902718 All cleanup done. Thu Nov 21 00:03:23 UTC 2024 - total duration: 0h 4m 10s. Thu Nov 21 00:03:23 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-FKIZvNV5, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 15.972s CPU time consumed: 8.540s