Fri Nov 29 08:51:27 UTC 2024 I: starting to build tombo/unstable/armhf on jenkins on '2024-11-29 08:51' Fri Nov 29 08:51:27 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_2/9271/console.log Fri Nov 29 08:51:27 UTC 2024 I: Downloading source for unstable/tombo=1.5.1-7 --2024-11-29 08:51:28-- 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% 311M=0s 2024-11-29 08:51:28 (311 MB/s) - ‘tombo_1.5.1-7.dsc’ saved [2267/2267] Fri Nov 29 08:51:28 UTC 2024 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----- Fri Nov 29 08:51:28 UTC 2024 I: Checking whether the package is not for us Fri Nov 29 08:51:28 UTC 2024 I: Starting 1st build on remote node virt32a-armhf-rb.debian.net. Fri Nov 29 08:51:28 UTC 2024 I: Preparing to do remote build '1' on virt32a-armhf-rb.debian.net. Fri Nov 29 09:00:36 UTC 2024 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 28 20:51:38 -12 2024 I: pbuilder-time-stamp: 1732870298 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 gpgv: Signature made Wed Nov 27 20:28:01 2024 gpgv: using RSA key 52D5BD0E7D4DB084E34B5865D4A41CFADDB20DB5 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-7.dsc: no acceptable signature found 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/7304/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='2c147abb52fb48898090965700958646' 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='7304' 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.V4xTwcOm/pbuilderrc_lXn0 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/b1 --logfile b1/build.log tombo_1.5.1-7.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7304/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: armhf 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 ... 19684 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} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libicu72{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} libldap-2.5-0{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{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} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{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-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} python3.12{a} python3.12-dev{a} python3.12-doc{a} python3.12-minimal{a} python3.13{a} python3.13-dev{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 publicsuffix python3-coverage python3-pil python3-pooch wget 0 packages upgraded, 149 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After unpacking 521 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.7-3 [800 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.7-3 [1808 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.7-1 [26.8 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-3 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 13 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.7-3 [1819 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.7-3 [671 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.7-1 [9712 B] Get: 23 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.7-1 [27.8 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.0-2 [843 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.0-2 [1691 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf sgml-base all 1.31 [15.4 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf openssl armhf 3.3.2-2 [1348 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf ca-certificates all 20240203 [158 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-11 [83.6 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf cython3 armhf 3.0.11+dfsg-1+b1 [2812 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 51 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 65 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 75.2.0-1 [213 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 75.2.0-1 [731 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20241024 [109 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf xml-core all 0.19 [20.1 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libaec0 armhf 1.1.3-1+b1 [21.9 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-4 [111 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.0-1 [303 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf libsz2 armhf 1.1.3-1+b1 [8036 B] Get: 90 http://deb.debian.org/debian unstable/main armhf libhdf5-103-1t64 armhf 1.10.10+repack-5 [1194 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf libhdf5-hl-100t64 armhf 1.10.10+repack-5 [62.1 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-4 [1828 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b2 [25.6 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf liblzf1 armhf 3.6-4+b2 [9260 B] Get: 100 http://deb.debian.org/debian unstable/main armhf libpython3.12t64 armhf 3.12.7-3 [1848 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libpython3.12-dev armhf 3.12.7-3 [3808 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf libpython3-dev armhf 3.12.7-1 [9976 B] Get: 104 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1850 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf libpython3.13 armhf 3.13.0-2 [1843 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf libpython3.13-dev armhf 3.13.0-2 [3781 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libpython3-all-dev armhf 3.12.7-1 [1072 B] Get: 108 http://deb.debian.org/debian unstable/main armhf python-babel-localedata all 2.16.0-1 [5696 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf python-requests-doc all 2.32.3+dfsg-1 [196 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.0-2 [730 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.12.7-1 [1052 B] Get: 113 http://deb.debian.org/debian unstable/main armhf python3.12-dev armhf 3.12.7-3 [505 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf python3-dev armhf 3.12.7-1 [26.1 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf python3.13-dev armhf 3.13.0-2 [504 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf python3-all-dev armhf 3.12.7-1 [1076 B] Get: 117 http://deb.debian.org/debian unstable/main armhf python3-babel all 2.16.0-1 [114 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 119 http://deb.debian.org/debian unstable/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf python3-charset-normalizer armhf 3.4.0-1+b1 [126 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf python3-decorator all 5.1.1-5 [15.1 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 123 http://deb.debian.org/debian unstable/main armhf python3.12-doc all 3.12.7-3 [13.4 MB] Get: 124 http://deb.debian.org/debian unstable/main armhf python3-doc all 3.12.7-1 [9900 B] Get: 125 http://deb.debian.org/debian unstable/main armhf python3-roman all 4.2-1 [10.4 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 127 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB] Get: 128 http://deb.debian.org/debian unstable/main armhf python3-h5py-serial armhf 3.11.0-8+b1 [1264 kB] Get: 129 http://deb.debian.org/debian unstable/main armhf python3-h5py all 3.11.0-8 [14.9 kB] Get: 130 http://deb.debian.org/debian unstable/main armhf python3-idna all 3.8-2 [41.6 kB] Get: 131 http://deb.debian.org/debian unstable/main armhf python3-imagesize all 1.4.1-1 [6688 B] Get: 132 http://deb.debian.org/debian unstable/main armhf python3-markupsafe armhf 2.1.5-1+b2 [13.4 kB] Get: 133 http://deb.debian.org/debian unstable/main armhf python3-jinja2 all 3.1.3-1 [119 kB] Get: 134 http://deb.debian.org/debian unstable/main armhf python3-mappy armhf 2.27+dfsg-1+b2 [173 kB] Get: 135 http://deb.debian.org/debian unstable/main armhf python3-nose2 all 0.14.0-2 [115 kB] Get: 136 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.2-1 [55.3 kB] Get: 137 http://deb.debian.org/debian unstable/main armhf python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 138 http://deb.debian.org/debian unstable/main armhf python3-urllib3 all 2.0.7-2 [111 kB] Get: 139 http://deb.debian.org/debian unstable/main armhf python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 140 http://deb.debian.org/debian unstable/main armhf python3-scipy armhf 1.14.1-2 [17.8 MB] Get: 141 http://deb.debian.org/debian unstable/main armhf python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 142 http://deb.debian.org/debian unstable/main armhf sphinx-common all 7.4.7-4 [731 kB] Get: 143 http://deb.debian.org/debian unstable/main armhf python3-sphinx all 7.4.7-4 [588 kB] Get: 144 http://deb.debian.org/debian unstable/main armhf python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 145 http://deb.debian.org/debian unstable/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 146 http://deb.debian.org/debian unstable/main armhf python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 147 http://deb.debian.org/debian unstable/main armhf python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 148 http://deb.debian.org/debian unstable/main armhf python3-tqdm all 4.67.1-1 [91.0 kB] Get: 149 http://deb.debian.org/debian unstable/main armhf sphinx-doc all 7.4.7-4 [3493 kB] Fetched 118 MB in 3s (37.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19684 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 libpython3.12-minimal:armhf. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.7-3) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_armhf.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:armhf (3.12.7-3) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20030 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_armhf.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../14-libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_armhf.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21092 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_armhf.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:armhf. Preparing to unpack .../001-libpython3.13-minimal_3.13.0-2_armhf.deb ... Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.0-2_armhf.deb ... Unpacking python3.13-minimal (3.13.0-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.2-2_armhf.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-11_armhf.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../014-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cython3. Preparing to unpack .../021-cython3_3.0.11+dfsg-1+b1_armhf.deb ... Unpacking cython3 (3.0.11+dfsg-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../022-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../023-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../024-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../025-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../026-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../027-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../028-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../029-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../030-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../031-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../032-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... 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Setting up libblas3:armhf (3.12.0-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libexpat1-dev:armhf (2.6.4-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up liblzf1:armhf (3.6-4+b2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up python3.13-minimal (3.13.0-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Setting up libsz2:armhf (1.1.3-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:armhf (3.12.0-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up python-requests-doc (2.32.3+dfsg-1) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up python3.12-doc (3.12.7-3) ... Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... Setting up python3-doc (3.12.7-1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ... Setting up libpython3.13:armhf (3.13.0-2) ... Setting up sphinx-doc (7.4.7-4) ... Setting up libcurl4t64:armhf (8.11.0-1) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3.13-dev:armhf (3.13.0-2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:armhf (1.10.10+repack-5) ... Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-5) ... Setting up libpython3.12-stdlib:armhf (3.12.7-3) ... Setting up python3.13-dev (3.13.0-2) ... Setting up python3.12 (3.12.7-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:armhf (3.12.7-3) ... Setting up libpython3-stdlib:armhf (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:armhf (3.12.7-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-3) ... Setting up cython3 (3.0.11+dfsg-1+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:armhf (3.12.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-2) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-tqdm (4.67.1-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-mappy (2.27+dfsg-1+b2) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:armhf (3.12.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.7-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-nose2 (0.14.0-2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.14.1-2) ... Setting up python3-h5py-serial (3.11.0-8+b1) ... Setting up python3-h5py (3.11.0-8) ... Processing triggers for libc-bin (2.40-4) ... 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 (7.4.7-4) ... 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-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 armhf 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:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running clean removing '/build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.12' 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:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /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/_version.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_helper.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/_event_resquiggle.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/_default_parameters.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/__init__.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/resquiggle.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 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:218: _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:218: _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-armv7l-cpython-313/tombo arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-armv7l-cpython-313/tombo/_c_dynamic_programming.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/python3/dist-packages/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 " \ | ^~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-313/tombo/_c_dynamic_programming.o -L/usr/lib/arm-linux-gnueabihf -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_dynamic_programming.cpython-313-arm-linux-gnueabihf.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 arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.13 -c tombo/_c_helper.cpp -o build/temp.linux-armv7l-cpython-313/tombo/_c_helper.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/python3/dist-packages/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 " \ | ^~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-313/tombo/_c_helper.o -L/usr/lib/arm-linux-gnueabihf -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.13/build/tombo/_c_helper.cpython-313-arm-linux-gnueabihf.so I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running build running build_py creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo copying tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo 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:218: _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:218: _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_3.12/build/tombo copying tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts creating /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models running build_ext building 'tombo._c_dynamic_programming' extension creating build/temp.linux-armv7l-cpython-312/tombo arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-armv7l-cpython-312/tombo/_c_dynamic_programming.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_dynamic_programming.cpp:1262: /usr/lib/python3/dist-packages/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 " \ | ^~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/tombo/_c_dynamic_programming.o -L/usr/lib/arm-linux-gnueabihf -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.cpython-312-arm-linux-gnueabihf.so building 'tombo._c_helper' extension arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c tombo/_c_helper.cpp -o build/temp.linux-armv7l-cpython-312/tombo/_c_helper.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5, from tombo/_c_helper.cpp:1262: /usr/lib/python3/dist-packages/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 " \ | ^~~~~~~ arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/tombo/_c_helper.o -L/usr/lib/arm-linux-gnueabihf -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.cpython-312-arm-linux-gnueabihf.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 v7.4.7 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' WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done 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 I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build; python3.12 -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/python3.13 setup.py install --root /build/reproducible-path/tombo-1.5.1/debian/tmp /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running 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:218: _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:218: _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/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/_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.cpython-313-arm-linux-gnueabihf.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/_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/_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_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/_c_helper.cpython-313-arm-linux-gnueabihf.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/_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/_event_resquiggle.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.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.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.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.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.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/_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/_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/_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/__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/_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/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/__main__.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/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/_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/_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_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/_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/_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/_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/_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/_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/__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/_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/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/__main__.py to __main__.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 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:261: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running 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:218: _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:218: _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/python3.12/dist-packages creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_stats.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_version.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.cpython-312-arm-linux-gnueabihf.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.cpython-312-arm-linux-gnueabihf.so -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_plot_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.pyx -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_helper.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_filter_reads.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_event_resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_option_parsers.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo creating /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSigMDS.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotPerReadStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotROCPerRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotReadCorr.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotGroupComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotMotifStats.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotKmerDist.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotModelComp.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSingleRun.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugFit.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotSingleRead.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/plotROC.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/R_scripts/debugRawDP.R -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/R_scripts copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_default_parameters.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_preprocess.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_text_output_commands.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/resquiggle.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo copying /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/__main__.py -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_version.py to _version.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_preprocess.py to _preprocess.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/resquiggle.py to resquiggle.cpython-312.pyc byte-compiling /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/__main__.py to __main__.cpython-312.pyc running install_egg_info Copying ont_tombo.egg-info to /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged 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' in '../tombo_1.5.1-7_armhf.deb'. dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_armhf.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_armhf.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_armhf.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/7304 and its subdirectories I: Current time: Thu Nov 28 20:59:43 -12 2024 I: pbuilder-time-stamp: 1732870783 Fri Nov 29 09:00:39 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64c-armhf-rb.debian.net. Fri Nov 29 09:00:39 UTC 2024 I: Preparing to do remote build '2' on virt64c-armhf-rb.debian.net. Fri Nov 29 09:18:17 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. Fri Nov 29 09:18:20 UTC 2024 I: tombo_1.5.1-7_armhf.changes: Format: 1.8 Date: Thu, 28 Nov 2024 01:40:55 +0530 Source: tombo Binary: tombo tombo-dbgsym tombo-doc Architecture: armhf 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: e85493ebd73290d93007a4b05a287d020ae745af 1133376 tombo-dbgsym_1.5.1-7_armhf.deb 8b6e31f6ff5cd026ea1481d2e9d3473bff5eff08 21734224 tombo-doc_1.5.1-7_all.deb 73847eeb25d95b20533e58962accffcb9d02c289 9200 tombo_1.5.1-7_armhf.buildinfo 59b20d446098e96f0fb0aa6c0ecb48f9448522c9 496760 tombo_1.5.1-7_armhf.deb Checksums-Sha256: 77b791897adf710d38e8252b55d058a7d888b2c38e084d1ef942b8d7bfe8b662 1133376 tombo-dbgsym_1.5.1-7_armhf.deb 328e86dd52929d9027bb39c9f6868f5a978e3a948ab07785740fe47c3dd6a15f 21734224 tombo-doc_1.5.1-7_all.deb 3e6fff19267fe835969c8426dd95738ca1b143298f5c47e418245aa0fcea7bc3 9200 tombo_1.5.1-7_armhf.buildinfo 6c6e6ccc6ab53f7400aba635d14d898d0e6fc611b339d7ccaa6a84f82daa47b7 496760 tombo_1.5.1-7_armhf.deb Files: 75ea7cfdc3c2d1d0fab6434e7bc1b565 1133376 debug optional tombo-dbgsym_1.5.1-7_armhf.deb d981fa9cf4517d143e3cfe169cb3a3da 21734224 doc optional tombo-doc_1.5.1-7_all.deb 361d0dd30f901fc6af8cfd09ab6117d0 9200 science optional tombo_1.5.1-7_armhf.buildinfo 479fc93e1da1deb29a331deb1c9275e6 496760 science optional tombo_1.5.1-7_armhf.deb Fri Nov 29 09:18:21 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_2-9271.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/tombo_1.5.1-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/tombo_1.5.1-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/tombo_1.5.1-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/b1/tombo_1.5.1-7_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.V4xTwcOm/b2/tombo_1.5.1-7_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.533s) 0.533s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.218s) 0.218s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 832ms CPU time consumed: 832ms Fri Nov 29 09:18:22 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 29 09:18:22 UTC 2024 I: tombo from unstable built successfully and reproducibly on armhf. Fri Nov 29 09:18:23 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 29 09:18:23 UTC 2024 I: Submitting 12K b1/tombo_1.5.1-7_armhf.buildinfo.asc Fri Nov 29 09:18:24 UTC 2024 I: Submitting 12K b2/tombo_1.5.1-7_armhf.buildinfo.asc Fri Nov 29 09:18:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 29 09:18:25 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 29 09:18:25 UTC 2024 I: Removing signed tombo_1.5.1-7_armhf.buildinfo.asc files: removed './b1/tombo_1.5.1-7_armhf.buildinfo.asc' removed './b2/tombo_1.5.1-7_armhf.buildinfo.asc'