Running as unit: rb-build-amd64_4-47396.service ==================================================================================== Mon Mar 10 18:50:19 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_4) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Mon Mar 10 18:50:19 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-7KOC0kbr" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Mar 10 18:50:19 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Mon Mar 10 18:50:19 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-eBBpIg' Mon Mar 10 18:50:19 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Mon Mar 10 18:50:19 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-eeJVyN' ok, let's check if tombo is building anywhere yet… ok, tombo is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of tombo in trixie on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Mon Mar 10 18:50:32 UTC 2025 I: starting to build tombo/trixie/amd64 on jenkins on '2025-03-10 18:50' Mon Mar 10 18:50:32 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/47396/console.log 1741632632 amd64 trixie tombo Mon Mar 10 18:50:32 UTC 2025 I: Downloading source for trixie/tombo=1.5.1-7 --2025-03-10 18:50:33-- http://deb.debian.org/debian/pool/main/t/tombo/tombo_1.5.1-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘tombo_1.5.1-7.dsc’ 0K .. 100% 347M=0s 2025-03-10 18:50:33 (347 MB/s) - ‘tombo_1.5.1-7.dsc’ saved [2267/2267] --2025-03-10 18:50:33-- http://deb.debian.org/debian/pool/main/t/tombo/tombo_1.5.1-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘tombo_1.5.1-7.dsc’ 0K .. 100% 347M=0s 2025-03-10 18:50:33 (347 MB/s) - ‘tombo_1.5.1-7.dsc’ saved [2267/2267] Mon Mar 10 18:50:33 UTC 2025 I: tombo_1.5.1-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tombo Binary: tombo, tombo-doc Architecture: any all Version: 1.5.1-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/nanoporetech/tombo Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/tombo Vcs-Git: https://salsa.debian.org/med-team/tombo.git Testsuite: autopkgtest Build-Depends: cython3, debhelper-compat (= 13), dh-python, libjs-mathjax, python3-all-dev, python3-h5py , python3-mappy , python3-nose2 , python3-numpy , python3-scipy , python3-setuptools, python3-sphinx, python3-sphinx-argparse, python3-sphinx-rtd-theme, python3-tqdm , sphinx-doc Package-List: tombo deb science optional arch=any tombo-doc deb doc optional arch=all Checksums-Sha1: 94f33539552d8c2f7e6c06987fd264400fc17f84 22294835 tombo_1.5.1.orig.tar.gz 89090ba7cc0a0903969d8a298637acb99145f93d 9528 tombo_1.5.1-7.debian.tar.xz Checksums-Sha256: f5f7ce37baee40b851ea867c2b835e6eae324ef90bdeb23fb931fde3272769a0 22294835 tombo_1.5.1.orig.tar.gz 7543db04f30121f2a2b5d22edb590a79b894b04dce37229f9bfd8c7a7baca8ea 9528 tombo_1.5.1-7.debian.tar.xz Files: 3709e4f4d6f4c58ec2d6ae216059929c 22294835 tombo_1.5.1.orig.tar.gz 7b8e973e64ac9656fdfb2238911c5920 9528 tombo_1.5.1-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEUtW9Dn1NsITjS1hl1KQc+t2yDbUFAmdHgNEACgkQ1KQc+t2y DbXhMRAAxgFk6YCm/LYGvd+RygfbLtS5kgD81CWOCUWZqP1rLidPkPhHWo4OQ40B BLtA29oiD0vpAhYIWLAR4Kq4l5IWj8RPGeOah82mQD/Br6njGQpgNOJHJhl9j89g ZPn6CJaJMiJH+w7RVB6mAeeABoOrjk7aoYkLJyK145fLfWY8YMtD50Z7PW1wZRA2 Z5AVpQd7dmf2cLYZL+5eOs/cmy2cjGhb9aNLjDTK3FSlQNdFj49pMBKMffI6JTRp ZikremJqmCTDMJ0bkBBkFBcgUiouHFPtZH2AY/JhK53x9ED4qRqXYGmBrDLX+S/Z ih6WNxsLk2Ohbki+wRclaCrQbCR8An9+cySGbfvo6lSHF+G46DCXeQOW+2SQ4TBe 7HyHMGGzB/cGjavwjp3ocJt/CzXUHNameKntmscU6cI/xhf7xknmB50JySXBQkjf VMobWR5MyDOKeCQnkhc9hXtcbKLmAKoTFKciCdj1tNGWhwBXG8xsoA6fNkACrLPR 0ofDvKv9csHyEZhZ65Pcq6HUT2V++8nOVaBYUKpP7QR4oCq06F3YNnkU8qVywMe/ re/iyNMxBzPCzpN8Kv0scMMD7Atgw3AhatG88TN/V/OdHa/cWxsI5WEDLPXkrYEV xNoJhJ6H5a7xaL+cISDkrYBmyl2pTF0CyLY8tXSrJGN2NLQTalU= =nPqk -----END PGP SIGNATURE----- Mon Mar 10 18:50:33 UTC 2025 I: Checking whether the package is not for us Mon Mar 10 18:50:33 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Mar 10 18:50:33 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Mar 10 18:50:33 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Mon Mar 10 18:50:33 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Xl3bXA' ==================================================================================== Mon Apr 13 01:13:31 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 tombo trixie /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk 1.5.1-7" as arguments. Mon Apr 13 01:13:31 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-V1IQbx5n" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Apr 13 01:13:31 UTC 2026 I: Downloading source for trixie/tombo=1.5.1-7 Reading package lists... NOTICE: 'tombo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tombo.git Please use: git clone https://salsa.debian.org/med-team/tombo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.3 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (dsc) [2267 B] Get:2 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (tar) [22.3 MB] Get:3 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (diff) [9528 B] Fetched 22.3 MB in 0s (51.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tombo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tombo.git Please use: git clone https://salsa.debian.org/med-team/tombo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.3 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (dsc) [2267 B] Get:2 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (tar) [22.3 MB] Get:3 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (diff) [9528 B] Fetched 22.3 MB in 0s (51.8 MB/s) Download complete and in download only mode ============================================================================= Building tombo in trixie on amd64 on ionos15-amd64 now. Date: Mon Apr 13 01:13:32 UTC 2026 Date UTC: Mon Apr 13 01:13:32 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 12 13:13:32 -12 2026 I: pbuilder-time-stamp: 1776042812 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 [tombo_1.5.1-7.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7.dsc: unsupported subcommand dpkg-source: info: extracting tombo in tombo-1.5.1 dpkg-source: info: unpacking tombo_1.5.1.orig.tar.gz dpkg-source: info: unpacking tombo_1.5.1-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_future.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying mathjax.patch dpkg-source: info: applying cython3-fix.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying remove-pkg-resources-usage.patch dpkg-source: info: applying remove-distutils-usage.patch dpkg-source: info: applying remove-badges-in-doc.patch dpkg-source: info: applying fix-invalid-escape-sequences.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a6f2478f67934dc9a62a342c0d6e5abb' 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='3068588' 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.39tqdZdk/pbuilderrc_ZqOz --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.39tqdZdk/b1 --logfile b1/build.log tombo_1.5.1-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cython3, debhelper-compat (= 13), dh-python, libjs-mathjax, python3-all-dev, python3-h5py, python3-mappy, python3-nose2, python3-numpy, python3-scipy, python3-setuptools, python3-sphinx, python3-sphinx-argparse, python3-sphinx-rtd-theme, python3-tqdm, sphinx-doc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19800 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-mappy; however: Package python3-mappy is not installed. pbuilder-satisfydepends-dummy depends on python3-nose2; however: Package python3-nose2 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc 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} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcares2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhdf5-310{a} libhdf5-hl-310{a} libicu72{a} libidn2-0{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap2{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libnode115{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsz2{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} node-acorn{a} node-balanced-match{a} node-brace-expansion{a} node-cjs-module-lexer{a} node-commander{a} node-corepack{a} node-mathjax-full{a} node-minimatch{a} node-mj-context-menu{a} node-speech-rule-engine{a} node-undici{a} node-xtend{a} nodejs{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-doc{a} python3-docutils{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-mappy{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-nose2{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-doc{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx nodejs-doc publicsuffix python3-coverage python3-pil python3-pooch wget 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After unpacking 619 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2+b1 [138 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-2+b1 [5081 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250108 [113 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 node-xtend all 4.0.2-3 [3932 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 node-corepack all 0.24.0-4 [704 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 nodejs amd64 20.18.3+dfsg-1 [349 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 node-balanced-match all 2.0.0-1 [4872 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B] Get: 113 http://deb.debian.org/debian trixie/main amd64 node-minimatch all 9.0.3-5 [76.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libnode115 amd64 20.18.3+dfsg-1 [12.1 MB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-1 [1068 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 node-commander all 9.4.1-1 [65.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 python-requests-doc all 2.32.3+dfsg-4 [196 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-1 [1048 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-1 [1068 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 python3.13-doc all 3.13.2-1 [15.3 MB] Get: 139 http://deb.debian.org/debian trixie/main amd64 python3-doc all 3.13.2-1 [10.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.13.0-1+b1 [1065 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.13.0-1 [15.0 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-mappy amd64 2.27+dfsg-1+b3 [149 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-nose2 all 0.15.1-1 [118 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-4+b1 [17.1 MB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] Fetched 135 MB in 2s (71.4 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19800 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up node-cjs-module-lexer (1.2.3+dfsg-1) ... Setting up node-mj-context-menu (0.9.1+ds-2) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 13 01:14:29 UTC 2026. Universal Time is now: Mon Apr 13 01:14:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up node-balanced-match (2.0.0-1) ... Setting up node-brace-expansion (2.0.1+~1.1.0-1) ... Setting up liblzf1:amd64 (3.6-4+b3) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libcares2:amd64 (1.34.4-2.1) ... Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2+b1) ... Setting up autopoint (0.23.1-1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up node-commander (9.4.1-1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up node-undici (7.3.0+dfsg1+~cs24.12.11-1) ... 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Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3.13-doc (3.13.2-1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up python-requests-doc (2.32.3+dfsg-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up python3-doc (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.2-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libpython3.13:amd64 (3.13.2-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-5) ... Setting up python3-idna (3.10-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-2+b1) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-scipy (1.14.1-4+b1) ... Setting up libpython3-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:amd64 (8.12.1-3) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-tqdm (4.67.1-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.2-1) ... Setting up debhelper (13.24.1) ... Setting up python3-mappy (2.27+dfsg-1+b3) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.2-1) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-all-dev (3.13.2-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-h5py-serial (3.13.0-1+b1) ... Setting up python3-nose2 (0.15.1-1) ... Setting up python3-h5py (3.13.0-1) ... Setting up dh-python (6.20250108) ... Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... Setting up node-corepack (0.24.0-4) ... Setting up libnode115:amd64 (20.18.3+dfsg-1) ... Setting up nodejs (20.18.3+dfsg-1) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up node-speech-rule-engine (4.0.7+~0.1.31-2) ... Setting up node-mathjax-full (3.2.2+~cs4.2.1-4) ... Setting up sphinx-doc (8.1.3-5) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/tombo-1.5.1/ && 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 > ../tombo_1.5.1-7_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt writing manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_dynamic_programming.pyx because it changed. [1/1] Cythonizing tombo/_c_dynamic_programming.pyx building 'tombo._c_dynamic_programming' extension creating build/temp.linux-x86_64-cpython-313/tombo x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_helper.pyx because it changed. [1/1] Cythonizing tombo/_c_helper.pyx building 'tombo._c_helper' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' sphinx-build -N -bhtml docs docs/build Running Sphinx v8.1.3 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 55%] plotting reading sources... [ 64%] resquiggle reading sources... [ 73%] rna reading sources... [ 82%] text_output reading sources... [ 91%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/language_data.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/basic.css Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 55%] plotting writing output... [ 64%] resquiggle writing output... [ 73%] rna writing output... [ 82%] text_output writing output... [ 91%] tombo writing output... [100%] tutorials generating indices... genindex done highlighting module code... writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 9%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 22%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 35%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 48%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 57%] _images/pre_read_5mC.png copying images... [ 61%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 70%] _images/kmer_levels.png copying images... [ 74%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 83%] _images/begin_half_z_scores.png copying images... [ 87%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 96%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 5 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build; python3.13 -m nose2 -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/resquiggle.py to resquiggle.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_preprocess.py to _preprocess.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-313.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f docs/tombo.rst rm -rf docs/build make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/tombo/usr/share/tombo/scripts/dump_per_read_statistics.py debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' find debian -name "*.model" -exec chmod -x {} \; find debian -name "shell_tests.sh" -type f -executable -exec chmod -x {} \+ make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 dpkg-gencontrol: warning: package tombo-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo' in '../tombo_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3068588 and its subdirectories I: Current time: Sun Apr 12 13:15:33 -12 2026 I: pbuilder-time-stamp: 1776042933 Mon Apr 13 01:15:33 UTC 2026 I: Signing ./b1/tombo_1.5.1-7_amd64.buildinfo as tombo_1.5.1-7_amd64.buildinfo.asc Mon Apr 13 01:15:33 UTC 2026 I: Signed ./b1/tombo_1.5.1-7_amd64.buildinfo as ./b1/tombo_1.5.1-7_amd64.buildinfo.asc Mon Apr 13 01:15:33 UTC 2026 - build #1 for tombo/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Mon Apr 13 01:15:33 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-V1IQbx5n, removing. /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Mar 10 18:52 b1 drwxr-xr-x 2 jenkins jenkins 4096 Mar 10 18:50 b2 -rw------- 1 jenkins jenkins 3350 Mar 10 18:50 rbuildlog.R1WR57k -rw-r--r-- 1 jenkins jenkins 2267 Nov 27 20:35 tombo_1.5.1-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b1: total 22388 -rw-r--r-- 1 jenkins jenkins 105738 Mar 10 18:52 build.log -rw-r--r-- 1 jenkins jenkins 578688 Mar 10 18:52 tombo-dbgsym_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 21734124 Mar 10 18:52 tombo-doc_1.5.1-7_all.deb -rw-r--r-- 1 jenkins jenkins 9528 Mar 10 18:52 tombo_1.5.1-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Mar 10 18:52 tombo_1.5.1-7.dsc -rw-r--r-- 1 jenkins jenkins 9481 Mar 10 18:52 tombo_1.5.1-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10363 Mar 10 18:52 tombo_1.5.1-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2308 Mar 10 18:52 tombo_1.5.1-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 449784 Mar 10 18:52 tombo_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1798 Mar 10 18:52 tombo_1.5.1-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b2: total 0 Mon Mar 10 18:52:36 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 12 13:13:32 -12 2026 I: pbuilder-time-stamp: 1776042812 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 [tombo_1.5.1-7.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7.dsc: unsupported subcommand dpkg-source: info: extracting tombo in tombo-1.5.1 dpkg-source: info: unpacking tombo_1.5.1.orig.tar.gz dpkg-source: info: unpacking tombo_1.5.1-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_future.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying mathjax.patch dpkg-source: info: applying cython3-fix.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying remove-pkg-resources-usage.patch dpkg-source: info: applying remove-distutils-usage.patch dpkg-source: info: applying remove-badges-in-doc.patch dpkg-source: info: applying fix-invalid-escape-sequences.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='a6f2478f67934dc9a62a342c0d6e5abb' 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='3068588' 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.39tqdZdk/pbuilderrc_ZqOz --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.39tqdZdk/b1 --logfile b1/build.log tombo_1.5.1-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cython3, debhelper-compat (= 13), dh-python, libjs-mathjax, python3-all-dev, python3-h5py, python3-mappy, python3-nose2, python3-numpy, python3-scipy, python3-setuptools, python3-sphinx, python3-sphinx-argparse, python3-sphinx-rtd-theme, python3-tqdm, sphinx-doc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19800 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-mappy; however: Package python3-mappy is not installed. pbuilder-satisfydepends-dummy depends on python3-nose2; however: Package python3-nose2 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc 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} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcares2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhdf5-310{a} libhdf5-hl-310{a} libicu72{a} libidn2-0{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap2{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libnode115{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsz2{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} node-acorn{a} node-balanced-match{a} node-brace-expansion{a} node-cjs-module-lexer{a} node-commander{a} node-corepack{a} node-mathjax-full{a} node-minimatch{a} node-mj-context-menu{a} node-speech-rule-engine{a} node-undici{a} node-xtend{a} nodejs{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-doc{a} python3-docutils{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-mappy{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-nose2{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-doc{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx nodejs-doc publicsuffix python3-coverage python3-pil python3-pooch wget 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After unpacking 619 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2+b1 [138 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-2+b1 [5081 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250108 [113 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 node-xtend all 4.0.2-3 [3932 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 node-corepack all 0.24.0-4 [704 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 nodejs amd64 20.18.3+dfsg-1 [349 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 node-balanced-match all 2.0.0-1 [4872 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B] Get: 113 http://deb.debian.org/debian trixie/main amd64 node-minimatch all 9.0.3-5 [76.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libnode115 amd64 20.18.3+dfsg-1 [12.1 MB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-1 [1068 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 node-commander all 9.4.1-1 [65.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 python-requests-doc all 2.32.3+dfsg-4 [196 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-1 [1048 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-1 [1068 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 python3.13-doc all 3.13.2-1 [15.3 MB] Get: 139 http://deb.debian.org/debian trixie/main amd64 python3-doc all 3.13.2-1 [10.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.13.0-1+b1 [1065 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.13.0-1 [15.0 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-mappy amd64 2.27+dfsg-1+b3 [149 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-nose2 all 0.15.1-1 [118 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-4+b1 [17.1 MB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] Fetched 135 MB in 2s (71.4 MB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3.13-doc (3.13.2-1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up python-requests-doc (2.32.3+dfsg-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up python3-doc (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.2-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libpython3.13:amd64 (3.13.2-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-5) ... Setting up python3-idna (3.10-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-2+b1) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-scipy (1.14.1-4+b1) ... Setting up libpython3-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:amd64 (8.12.1-3) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-tqdm (4.67.1-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.2-1) ... Setting up debhelper (13.24.1) ... Setting up python3-mappy (2.27+dfsg-1+b3) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.2-1) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-all-dev (3.13.2-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-h5py-serial (3.13.0-1+b1) ... Setting up python3-nose2 (0.15.1-1) ... Setting up python3-h5py (3.13.0-1) ... Setting up dh-python (6.20250108) ... Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... Setting up node-corepack (0.24.0-4) ... Setting up libnode115:amd64 (20.18.3+dfsg-1) ... Setting up nodejs (20.18.3+dfsg-1) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up node-speech-rule-engine (4.0.7+~0.1.31-2) ... Setting up node-mathjax-full (3.2.2+~cs4.2.1-4) ... Setting up sphinx-doc (8.1.3-5) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/tombo-1.5.1/ && 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 > ../tombo_1.5.1-7_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt writing manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_dynamic_programming.pyx because it changed. [1/1] Cythonizing tombo/_c_dynamic_programming.pyx building 'tombo._c_dynamic_programming' extension creating build/temp.linux-x86_64-cpython-313/tombo x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_helper.pyx because it changed. [1/1] Cythonizing tombo/_c_helper.pyx building 'tombo._c_helper' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' sphinx-build -N -bhtml docs docs/build Running Sphinx v8.1.3 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 55%] plotting reading sources... [ 64%] resquiggle reading sources... [ 73%] rna reading sources... [ 82%] text_output reading sources... [ 91%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/language_data.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/basic.css Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 55%] plotting writing output... [ 64%] resquiggle writing output... [ 73%] rna writing output... [ 82%] text_output writing output... [ 91%] tombo writing output... [100%] tutorials generating indices... genindex done highlighting module code... writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 9%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 22%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 35%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 48%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 57%] _images/pre_read_5mC.png copying images... [ 61%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 70%] _images/kmer_levels.png copying images... [ 74%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 83%] _images/begin_half_z_scores.png copying images... [ 87%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 96%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 5 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build; python3.13 -m nose2 -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/resquiggle.py to resquiggle.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_preprocess.py to _preprocess.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-313.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f docs/tombo.rst rm -rf docs/build make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/tombo/usr/share/tombo/scripts/dump_per_read_statistics.py debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' find debian -name "*.model" -exec chmod -x {} \; find debian -name "shell_tests.sh" -type f -executable -exec chmod -x {} \+ make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 dpkg-gencontrol: warning: package tombo-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo' in '../tombo_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3068588 and its subdirectories I: Current time: Sun Apr 12 13:15:33 -12 2026 I: pbuilder-time-stamp: 1776042933 Mon Mar 10 18:52:37 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Mar 10 18:52:37 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Mar 10 18:52:37 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Mon Mar 10 18:52:37 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-8a0nHI' ==================================================================================== Mon Mar 10 18:52:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "2 tombo trixie /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk 1.5.1-7" as arguments. Mon Mar 10 18:52:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-kfqoB2AR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Mar 10 18:52:38 UTC 2025 I: Downloading source for trixie/tombo=1.5.1-7 Reading package lists... NOTICE: 'tombo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tombo.git Please use: git clone https://salsa.debian.org/med-team/tombo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.3 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (dsc) [2267 B] Get:2 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (tar) [22.3 MB] Get:3 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (diff) [9528 B] Fetched 22.3 MB in 0s (62.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tombo' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tombo.git Please use: git clone https://salsa.debian.org/med-team/tombo.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 22.3 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (dsc) [2267 B] Get:2 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (tar) [22.3 MB] Get:3 http://deb.debian.org/debian trixie/main tombo 1.5.1-7 (diff) [9528 B] Fetched 22.3 MB in 0s (62.8 MB/s) Download complete and in download only mode ============================================================================= Re-Building tombo in trixie on amd64 on ionos1-amd64 now. Date: Mon Mar 10 18:52:39 UTC 2025 Date UTC: Mon Mar 10 18:52:39 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/pbuilderrc_60jn + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' tombo = debian-installer -o tombo = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' tombo = u-boot ']' + case "${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.39tqdZdk/pbuilderrc_60jn --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.39tqdZdk/b2 --logfile b2/build.log tombo_1.5.1-7.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: Tue Mar 11 08:52:40 +14 2025 I: pbuilder-time-stamp: 1741632760 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 [tombo_1.5.1-7.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-7.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7.dsc: unsupported subcommand dpkg-source: info: extracting tombo in tombo-1.5.1 dpkg-source: info: unpacking tombo_1.5.1.orig.tar.gz dpkg-source: info: unpacking tombo_1.5.1-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_future.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying mathjax.patch dpkg-source: info: applying cython3-fix.patch dpkg-source: info: applying no_install_depends_cython.patch dpkg-source: info: applying remove-pkg-resources-usage.patch dpkg-source: info: applying remove-distutils-usage.patch dpkg-source: info: applying remove-badges-in-doc.patch dpkg-source: info: applying fix-invalid-escape-sequences.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Mar 10 18:53 /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/3702184/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=de87e1b13c6343eb9a562c78212302cc LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=3702184 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.39tqdZdk/pbuilderrc_60jn --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.39tqdZdk/b2 --logfile b2/build.log tombo_1.5.1-7.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cython3, debhelper-compat (= 13), dh-python, libjs-mathjax, python3-all-dev, python3-h5py, python3-mappy, python3-nose2, python3-numpy, python3-scipy, python3-setuptools, python3-sphinx, python3-sphinx-argparse, python3-sphinx-rtd-theme, python3-tqdm, sphinx-doc dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19800 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 cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-mappy; however: Package python3-mappy is not installed. pbuilder-satisfydepends-dummy depends on python3-nose2; however: Package python3-nose2 is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however: Package python3-sphinx-rtd-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc 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} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcares2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhdf5-310{a} libhdf5-hl-310{a} libicu72{a} libidn2-0{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} libldap2{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libnode115{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsz2{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} node-acorn{a} node-balanced-match{a} node-brace-expansion{a} node-cjs-module-lexer{a} node-commander{a} node-corepack{a} node-mathjax-full{a} node-minimatch{a} node-mj-context-menu{a} node-speech-rule-engine{a} node-undici{a} node-xtend{a} nodejs{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-doc{a} python3-docutils{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-mappy{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-nose2{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-tqdm{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-doc{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx nodejs-doc publicsuffix python3-coverage python3-pil python3-pooch wget 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After unpacking 619 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-1 [28.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2+b1 [138 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:2.2.3+ds-2+b1 [5081 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.8.0-1 [724 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20250108 [113 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 96 http://deb.debian.org/debian trixie/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b3 [10.1 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 node-xtend all 4.0.2-3 [3932 B] Get: 107 http://deb.debian.org/debian trixie/main amd64 node-corepack all 0.24.0-4 [704 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 nodejs amd64 20.18.3+dfsg-1 [349 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 node-balanced-match all 2.0.0-1 [4872 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B] Get: 113 http://deb.debian.org/debian trixie/main amd64 node-minimatch all 9.0.3-5 [76.7 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libnode115 amd64 20.18.3+dfsg-1 [12.1 MB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.13.2-1 [1068 B] Get: 121 http://deb.debian.org/debian trixie/main amd64 node-commander all 9.4.1-1 [65.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 python-requests-doc all 2.32.3+dfsg-4 [196 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.13.2-1 [1048 B] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.13.2-1 [1068 B] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 python3.13-doc all 3.13.2-1 [15.3 MB] Get: 139 http://deb.debian.org/debian trixie/main amd64 python3-doc all 3.13.2-1 [10.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.13.0-1+b1 [1065 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.13.0-1 [15.0 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-mappy amd64 2.27+dfsg-1+b3 [149 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-nose2 all 0.15.1-1 [118 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.14.1-4+b1 [17.1 MB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] Fetched 135 MB in 18s (7291 kB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19800 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20160 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.2-1_amd64.deb ... Unpacking python3-minimal (3.13.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.50.0-2) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up node-cjs-module-lexer (1.2.3+dfsg-1) ... Setting up node-mj-context-menu (0.9.1+ds-2) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.17.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Mar 10 18:57:29 UTC 2025. Universal Time is now: Mon Mar 10 18:57:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up node-balanced-match (2.0.0-1) ... Setting up node-brace-expansion (2.0.1+~1.1.0-1) ... Setting up liblzf1:amd64 (3.6-4+b3) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libcares2:amd64 (1.34.4-2.1) ... Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-2+b1) ... Setting up autopoint (0.23.1-1) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up node-commander (9.4.1-1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up node-undici (7.3.0+dfsg1+~cs24.12.11-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... Setting up node-minimatch (9.0.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up node-xtend (4.0.2-3) ... Setting up openssl (3.4.1-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3.13-doc (3.13.2-1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up python-requests-doc (2.32.3+dfsg-4) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up xml-core (0.19) ... Setting up libpython3.13-stdlib:amd64 (3.13.2-1) ... Setting up python3-doc (3.13.2-1) ... Setting up libpython3-stdlib:amd64 (3.13.2-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libpython3.13:amd64 (3.13.2-1) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up python3.13 (3.13.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up python3-roman (5.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libpython3.13-dev:amd64 (3.13.2-1) ... Setting up sphinx-common (8.1.3-5) ... Setting up python3-idna (3.10-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-numpy (1:2.2.3+ds-2+b1) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-scipy (1.14.1-4+b1) ... Setting up libpython3-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up libcurl4t64:amd64 (8.12.1-3) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3.13-dev (3.13.2-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-tqdm (4.67.1-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up python3-all (3.13.2-1) ... Setting up debhelper (13.24.1) ... Setting up python3-mappy (2.27+dfsg-1+b3) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.13.2-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.2-1) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up python3-pkg-resources (75.8.0-1) ... Setting up python3-all-dev (3.13.2-1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up python3-setuptools (75.8.0-1) ... Setting up python3-h5py-serial (3.13.0-1+b1) ... Setting up python3-nose2 (0.15.1-1) ... Setting up python3-h5py (3.13.0-1) ... Setting up dh-python (6.20250108) ... Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... Setting up node-corepack (0.24.0-4) ... Setting up libnode115:amd64 (20.18.3+dfsg-1) ... Setting up nodejs (20.18.3+dfsg-1) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up node-speech-rule-engine (4.0.7+~0.1.31-2) ... Setting up node-mathjax-full (3.2.2+~cs4.2.1-4) ... Setting up sphinx-doc (8.1.3-5) ... Processing triggers for libc-bin (2.40-7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-argparse (0.5.2-1) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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/3702184/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/tombo-1.5.1/ && 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 > ../tombo_1.5.1-7_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt writing manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_dynamic_programming.pyx because it changed. [1/1] Cythonizing tombo/_c_dynamic_programming.pyx building 'tombo._c_dynamic_programming' extension creating build/temp.linux-x86_64-cpython-313/tombo x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_dynamic_programming.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_helper.pyx because it changed. [1/1] Cythonizing tombo/_c_helper.pyx building 'tombo._c_helper' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c tombo/_c_helper.cpp -o build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/tombo/_c_helper.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' sphinx-build -N -bhtml docs docs/build Running Sphinx v8.1.3 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 55%] plotting reading sources... [ 64%] resquiggle reading sources... [ 73%] rna reading sources... [ 82%] text_output reading sources... [ 91%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/language_data.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/basic.css Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 55%] plotting writing output... [ 64%] resquiggle writing output... [ 73%] rna writing output... [ 82%] text_output writing output... [ 91%] tombo writing output... [100%] tutorials generating indices... genindex done highlighting module code... writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 9%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 22%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 35%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 48%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 57%] _images/pre_read_5mC.png copying images... [ 61%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 70%] _images/kmer_levels.png copying images... [ 74%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 83%] _images/begin_half_z_scores.png copying images... [ 87%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 96%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 5 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build; python3.13 -m nose2 -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:79: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ont_tombo.egg-info/PKG-INFO writing dependency_links to ont_tombo.egg-info/dependency_links.txt writing entry points to ont_tombo.egg-info/entry_points.txt writing requirements to ont_tombo.egg-info/requires.txt writing top-level names to ont_tombo.egg-info/top_level.txt reading manifest file 'ont_tombo.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*' under directory 'cython' adding license file 'LICENSE.md' writing manifest file 'ont_tombo.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.R_scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.R_scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.R_scripts' to be distributed and are already explicitly excluding 'tombo.R_scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'tombo.tombo_models' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'tombo.tombo_models' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'tombo.tombo_models' to be distributed and are already explicitly excluding 'tombo.tombo_models' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) running build_ext running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_preprocess.py to _preprocess.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/resquiggle.py to resquiggle.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__main__.py to __main__.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-313.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' rm -f docs/tombo.rst rm -rf docs/build make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_installdocs -O--buildsystem=pybuild dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/tombo/usr/share/tombo/scripts/dump_per_read_statistics.py debian/rules execute_after_dh_python3 make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' find debian -name "*.model" -exec chmod -x {} \; find debian -name "shell_tests.sh" -type f -executable -exec chmod -x {} \+ make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' 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 dpkg-gencontrol: warning: package tombo-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo' in '../tombo_1.5.1-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3702184/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/3702184 and its subdirectories I: Current time: Tue Mar 11 09:07:07 +14 2025 I: pbuilder-time-stamp: 1741633627 + false + set +x Mon Mar 10 19:07:07 UTC 2025 I: Signing ./b2/tombo_1.5.1-7_amd64.buildinfo as tombo_1.5.1-7_amd64.buildinfo.asc Mon Mar 10 19:07:07 UTC 2025 I: Signed ./b2/tombo_1.5.1-7_amd64.buildinfo as ./b2/tombo_1.5.1-7_amd64.buildinfo.asc Mon Mar 10 19:07:07 UTC 2025 - build #2 for tombo/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Mon Mar 10 19:07:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-kfqoB2AR, removing. /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk: total 124 drwxr-xr-x 2 jenkins jenkins 4096 Mar 10 18:52 b1 drwxr-xr-x 2 jenkins jenkins 4096 Mar 10 19:07 b2 -rw------- 1 jenkins jenkins 109375 Mar 10 18:52 rbuildlog.R1WR57k -rw-r--r-- 1 jenkins jenkins 2267 Nov 27 20:35 tombo_1.5.1-7.dsc /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b1: total 22428 -rw-r--r-- 1 jenkins jenkins 105738 Mar 10 18:52 build.log -rw-r--r-- 1 jenkins jenkins 578688 Mar 10 18:52 tombo-dbgsym_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 21734124 Mar 10 18:52 tombo-doc_1.5.1-7_all.deb -rw-r--r-- 1 jenkins jenkins 9528 Mar 10 18:52 tombo_1.5.1-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Mar 10 18:52 tombo_1.5.1-7.dsc -rw-r--r-- 1 jenkins jenkins 9481 Mar 10 18:52 tombo_1.5.1-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10363 Mar 10 18:52 tombo_1.5.1-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2308 Mar 10 18:52 tombo_1.5.1-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 449784 Mar 10 18:52 tombo_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1798 Mar 10 18:52 tombo_1.5.1-7_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b2: total 22392 -rw-r--r-- 1 jenkins jenkins 107655 Mar 10 19:07 build.log -rw-r--r-- 1 jenkins jenkins 578688 Mar 10 19:07 tombo-dbgsym_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 21734124 Mar 10 19:07 tombo-doc_1.5.1-7_all.deb -rw-r--r-- 1 jenkins jenkins 9528 Mar 10 19:07 tombo_1.5.1-7.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Mar 10 19:07 tombo_1.5.1-7.dsc -rw-r--r-- 1 jenkins jenkins 9470 Mar 10 19:07 tombo_1.5.1-7_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 10352 Mar 10 19:07 tombo_1.5.1-7_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2308 Mar 10 19:07 tombo_1.5.1-7_amd64.changes -rw-r--r-- 1 jenkins jenkins 449784 Mar 10 19:07 tombo_1.5.1-7_amd64.deb -rw-r--r-- 1 jenkins jenkins 1798 Mar 10 19:07 tombo_1.5.1-7_source.changes Mon Mar 10 19:07:08 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Mar 10 19:07:08 UTC 2025 I: tombo_1.5.1-7_amd64.changes: Format: 1.8 Date: Thu, 28 Nov 2024 01:40:55 +0530 Source: tombo Binary: tombo tombo-dbgsym tombo-doc Architecture: amd64 all Version: 1.5.1-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Ananthu C V Description: tombo - identification of modified nucleotides from raw nanopore sequenci tombo-doc - identification of modified nucleotides from raw nanopore sequenci Closes: 1049071 1083801 1087117 Changes: tombo (1.5.1-7) unstable; urgency=medium . * Team upload * Use execute_after hooks instead of overriding targets * Remove built doc files from debian source tree after they are installed * Make sure to clean built files before next build (Closes: #1049071) * Add patch to use importlib instead of deprecated pkg_resources (Closes: #1083801) * Correct patch header metadata * Add patch to drop distutils usage * Apply wrap-and-sort * Fix installed file permissions * Add patch to remove badges from built docs * Add patch to fix invalid escape sequence syntax warnings (Closes: #1087117) * Bump Standards-Version to 4.7.0 (no changes needed) Checksums-Sha1: d91bdd3cabd4ab45a7090443345c39fdd5e88dec 578688 tombo-dbgsym_1.5.1-7_amd64.deb 687ad6b4c96cd482bad28f8289df55f9578f6a10 21734124 tombo-doc_1.5.1-7_all.deb 73c75615d26b190623df3912d7d1df0154456a86 9481 tombo_1.5.1-7_amd64.buildinfo 7b1832ed665f0d6b279911e2626c297e6910f460 449784 tombo_1.5.1-7_amd64.deb Checksums-Sha256: fefe6d31a23219b6f4277c7a18700efe611e54d9466682ea0ea86957b63f63e7 578688 tombo-dbgsym_1.5.1-7_amd64.deb ed37fbd47bf1b67634ac4f30091edff419e2604123f5aacd85df81d5c6fabe6b 21734124 tombo-doc_1.5.1-7_all.deb a40fb16bfb21fd795f14a8b223e35527045d131f031ca55711e420042d50a691 9481 tombo_1.5.1-7_amd64.buildinfo c28b44ac43a02d9dc472ac5da389a3b9d7998d973587598382be357b87cf8f91 449784 tombo_1.5.1-7_amd64.deb Files: cca1852e5290dd2647c0830a406b0fd0 578688 debug optional tombo-dbgsym_1.5.1-7_amd64.deb 61948dbff86ec1e09ff6621173f0b481 21734124 doc optional tombo-doc_1.5.1-7_all.deb 59f4dc7ada400817cb14cd8f449f3643 9481 science optional tombo_1.5.1-7_amd64.buildinfo 53bd2aa939f901b3e1a9ccb0750a15e4 449784 science optional tombo_1.5.1-7_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tombo_1.5.1-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tombo_1.5.1-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/tombo_1.5.1-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/tombo_1.5.1-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/tombo_1.5.1-7_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tombo_1.5.1-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-03-10 18:52:36.333902170 +0000 +++ b2/build.log 2025-03-10 19:07:07.934513105 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 12 13:13:32 -12 2026 -I: pbuilder-time-stamp: 1776042812 +I: Current time: Tue Mar 11 08:52:40 +14 2025 +I: pbuilder-time-stamp: 1741632760 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 fix-invalid-escape-sequences.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 Mar 10 18:53 /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/3702184/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a6f2478f67934dc9a62a342c0d6e5abb' - 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='3068588' - PS1='# ' - PS2='> ' + INVOCATION_ID=de87e1b13c6343eb9a562c78212302cc + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=3702184 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.39tqdZdk/pbuilderrc_ZqOz --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.39tqdZdk/b1 --logfile b1/build.log tombo_1.5.1-7.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.39tqdZdk/pbuilderrc_60jn --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.39tqdZdk/b2 --logfile b2/build.log tombo_1.5.1-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3068588/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -306,7 +338,7 @@ Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.1-2 [91.1 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] -Fetched 135 MB in 2s (71.4 MB/s) +Fetched 135 MB in 18s (7291 kB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19800 files and directories currently installed.) @@ -838,8 +870,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 13 01:14:29 UTC 2026. -Universal Time is now: Mon Apr 13 01:14:29 UTC 2026. +Local time is now: Mon Mar 10 18:57:29 UTC 2025. +Universal Time is now: Mon Mar 10 18:57:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -998,7 +1030,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tombo-1.5.1/ && 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 > ../tombo_1.5.1-7_source.changes +I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3702184/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tombo-1.5.1/ && 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 > ../tombo_1.5.1-7_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-7 dpkg-buildpackage: info: source distribution unstable @@ -1043,19 +1079,19 @@ running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo +copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo -copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo running egg_info creating ont_tombo.egg-info writing ont_tombo.egg-info/PKG-INFO @@ -1247,9 +1283,9 @@ preparing documents... done copying assets... copying static files... -Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/language_data.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/basic.css +Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/js/versions.js copying static files: done copying extra files... @@ -1429,62 +1465,62 @@ running install_lib creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_models +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/R_scripts +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo +copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__main__.py to __main__.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/resquiggle.py to resquiggle.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_preprocess.py to _preprocess.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_version.py to _version.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__init__.py to __init__.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/resquiggle.py to resquiggle.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/__main__.py to __main__.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-313.pyc +byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_version.py to _version.cpython-313.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-313.pyc -byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-313.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.13/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt @@ -1528,9 +1564,9 @@ dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild +dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_amd64.deb'. dpkg-deb: building package 'tombo' in '../tombo_1.5.1-7_amd64.deb'. -dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1538,12 +1574,14 @@ 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/3702184/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3702184/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/3068588 and its subdirectories -I: Current time: Sun Apr 12 13:15:33 -12 2026 -I: pbuilder-time-stamp: 1776042933 +I: removing directory /srv/workspace/pbuilder/3702184 and its subdirectories +I: Current time: Tue Mar 11 09:07:07 +14 2025 +I: pbuilder-time-stamp: 1741633627 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tombo_1.5.1-7.diff: 85.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/tombo_1.5.1-7.diff.gz b2/build.log: 84.2% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.6% -- replaced with stdout Mon Mar 10 19:07:09 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_tombo_trixie_amd64_1741633629 + touch /var/log/reproducible-builds/diffoscope_stamp_tombo_trixie_amd64_1741633629 + RESULT=0 + systemd-run '--description=diffoscope on tombo/1.5.1-7 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_4-47396 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk --run-session -c jenkins-reproducible-trixie-diffoscope-477ddde6-52fa-4eb7-a36d-efa5a3522175 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/dbd-tmp-qJaUQyW ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b1/tombo_1.5.1-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b2/tombo_1.5.1-7_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_4-47396.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/tombo_1.5.1-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b1/tombo_1.5.1-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.39tqdZdk/b2/tombo_1.5.1-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 224ms CPU time consumed: 225ms _ _ | |_ ___ _ __ ___ | |__ ___ | __/ _ \| '_ ` _ \| '_ \ / _ \ | || (_) | | | | | | |_) | (_) | \__\___/|_| |_| |_|_.__/ \___/ Mon Mar 10 19:07:10 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Mon Mar 10 19:07:10 UTC 2025 I: tombo from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-03-10 19:07:11] INFO: Starting at 2025-03-10 19:07:11.038251 [2025-03-10 19:07:11] INFO: Generating the pages of 1 package(s) [2025-03-10 19:07:11] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/tombo didn't produce a buildlog, even though it has been built. [2025-03-10 19:07:11] INFO: Finished at 2025-03-10 19:07:11.393267, took: 0:00:00.355024 Mon Mar 10 19:07:11 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/tombo.html Mon Mar 10 19:07:11 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Mar 10 19:07:11 UTC 2025 I: Submitting 12K b1/tombo_1.5.1-7_amd64.buildinfo.asc https://buildinfo.debian.net/73c75615d26b190623df3912d7d1df0154456a86/tombo_1.5.1-7_all Mon Mar 10 19:07:12 UTC 2025 I: Submitting 12K b2/tombo_1.5.1-7_amd64.buildinfo.asc https://buildinfo.debian.net/9287ad8c95cd63e3d99c06313a6f23d60f5c9a98/tombo_1.5.1-7_all Mon Mar 10 19:07:13 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Mar 10 19:07:13 UTC 2025 I: Done submitting .buildinfo files. Mon Mar 10 19:07:13 UTC 2025 I: Removing signed tombo_1.5.1-7_amd64.buildinfo.asc files: removed './b1/tombo_1.5.1-7_amd64.buildinfo.asc' removed './b2/tombo_1.5.1-7_amd64.buildinfo.asc' 1741633633 amd64 trixie tombo Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tombo_1.5.1-7.rbuild.log: 82.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/tombo_1.5.1-7.rbuild.log.gz [2025-03-10 19:07:13] INFO: Starting at 2025-03-10 19:07:13.389645 [2025-03-10 19:07:13] INFO: Generating the pages of 1 package(s) [2025-03-10 19:07:13] INFO: Finished at 2025-03-10 19:07:13.716621, took: 0:00:00.326982 All cleanup done. Mon Mar 10 19:07:13 UTC 2025 - total duration: 0h 16m 51s. Mon Mar 10 19:07:13 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-7KOC0kbr, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 16min 54.727s CPU time consumed: 7.404s