I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 22 14:47:29 +14 2026 I: pbuilder-time-stamp: 1769042849 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tombo_1.5.1-7.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-7.debian.tar.xz] I: Extracting source 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/1999892/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 22 00:47 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=4535ccb2d1354ddb8cc780387bdea073 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1999892 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.JxywFFZi/pbuilderrc_vaBO --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JxywFFZi/b2 --logfile b2/build.log tombo_1.5.1-7.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: 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 ... 20076 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} 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} 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, 142 newly installed, 0 to remove and 0 not upgraded. Need to get 109 MB of archives. After unpacking 552 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-3 [810 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-3 [1941 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-3 [1906 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-3 [677 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.3.2-2 [1347 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 cython3 arm64 3.0.11+dfsg-1+b1 [2726 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 63 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20241024 [109 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1 [325 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 88 http://deb.debian.org/debian trixie/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-5+b1 [1050 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-5+b1 [61.2 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b2 [25.6 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 liblzf1 arm64 3.6-4+b2 [10.0 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libpython3.12t64 arm64 3.12.8-3 [1983 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libpython3.12-dev arm64 3.12.8-3 [4823 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libpython3-dev arm64 3.12.6-1 [9952 B] Get: 102 http://deb.debian.org/debian trixie/main arm64 libpython3-all-dev arm64 3.12.6-1 [1064 B] Get: 103 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 python-requests-doc all 2.32.3+dfsg-1 [196 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 107 http://deb.debian.org/debian trixie/main arm64 python3.12-dev arm64 3.12.8-3 [505 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 python3-dev arm64 3.12.6-1 [26.1 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 python3-all-dev arm64 3.12.6-1 [1068 B] Get: 110 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 112 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 python3.12-doc all 3.12.8-3 [13.4 MB] Get: 117 http://deb.debian.org/debian trixie/main arm64 python3-doc all 3.12.6-1 [9884 B] Get: 118 http://deb.debian.org/debian trixie/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 python3-h5py-serial arm64 3.12.1-1 [1244 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 python3-h5py all 3.12.1-1 [15.0 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 125 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 python3-mappy arm64 2.27+dfsg-1+b3 [158 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 python3-nose2 all 0.14.0-2 [115 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.2.3-4 [112 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.14.1-3 [18.5 MB] Get: 134 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-2 [616 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-2 [468 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-argparse all 0.5.2-1 [59.6 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-tqdm all 4.67.1-1 [91.0 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 sphinx-doc all 8.1.3-2 [3487 kB] Fetched 109 MB in 1s (90.8 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 ... 20076 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:arm64. Preparing to unpack .../libpython3.12-minimal_3.12.8-3_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-3) ... Selecting previously unselected package libexpat1:arm64. 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Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. 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Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jan 22 00:48:32 UTC 2026. Universal Time is now: Thu Jan 22 00:48:32 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.6.4-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up liblzf1:arm64 (3.6-4+b2) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:arm64 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libjson-perl (4.10000-1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (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 (8.2-6) ... Setting up libxml2:arm64 (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:arm64 (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:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libldap-2.5-0:arm64 (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:arm64 (1.21.3-3) ... Setting up libjs-sphinxdoc (8.1.3-2) ... Setting up python-requests-doc (2.32.3+dfsg-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up python3.12-doc (3.12.8-3) ... Setting up python3-doc (3.12.6-1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b2) ... Setting up sphinx-doc (8.1.3-2) ... Setting up libcurl4t64:arm64 (8.11.1-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... 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 sphinx-common (8.1.3-2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-5+b1) ... Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-5+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-3) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:arm64 (3.12.8-3) ... Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:arm64 (3.12.8-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b3) ... 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 (3.12.8-3) ... Setting up cython3 (3.0.11+dfsg-1+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libpython3-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... 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 (3.12.6-1) ... Setting up python3-mappy (2.27+dfsg-1+b3) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:arm64 (3.12.6-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.6-1) ... 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 (1.14.1-3) ... Setting up python3-h5py-serial (3.12.1-1) ... Setting up python3-h5py (3.12.1-1) ... 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 (8.1.3-2) ... 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: user script /srv/workspace/pbuilder/1999892/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/tombo-1.5.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../tombo_1.5.1-7_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild 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-aarch64' 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: python3.12 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 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/_plot_commands.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/_preprocess.py -> /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/resquiggle.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/_version.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/_option_parsers.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/_default_parameters.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 copying tombo/__init__.py -> /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/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_3.12/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 /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-aarch64-cpython-312/tombo aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-aarch64-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 " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/tombo/_c_dynamic_programming.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_dynamic_programming.cpython-312-aarch64-linux-gnu.so /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling tombo/_c_helper.pyx because it changed. [1/1] Cythonizing tombo/_c_helper.pyx building 'tombo._c_helper' extension aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-aarch64-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 " \ | ^~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/tombo-1.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/tombo/_c_helper.o -L/usr/lib/aarch64-linux-gnu -o /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/build/tombo/_c_helper.cpython-312-aarch64-linux-gnu.so debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/tombo-1.5.1' sphinx-build -N -bhtml docs docs/build Running Sphinx v8.1.3 WARNING: Calling get_html_theme_path is deprecated. If you are calling it to define html_theme_path, you are safe to remove that code. loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] examples reading sources... [ 18%] filtering reading sources... [ 27%] index reading sources... [ 36%] model_training reading sources... [ 45%] modified_base_detection reading sources... [ 55%] plotting reading sources... [ 64%] resquiggle reading sources... [ 73%] rna reading sources... [ 82%] text_output reading sources... [ 91%] tombo reading sources... [100%] tutorials WARNING: autodoc: failed to import module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'resquiggle' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_helper' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] WARNING: autodoc: failed to import module 'tombo_stats' from module 'tombo'; the following exception was raised: No module named 'tombo' [autodoc.import_object] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/language_data.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/basic.css Writing evaluated template result to /build/reproducible-path/tombo-1.5.1/docs/build/_static/js/versions.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 9%] examples writing output... [ 18%] filtering writing output... [ 27%] index writing output... [ 36%] model_training writing output... [ 45%] modified_base_detection writing output... [ 55%] plotting writing output... [ 64%] resquiggle writing output... [ 73%] rna writing output... [ 82%] text_output writing output... [ 91%] tombo writing output... [100%] tutorials generating indices... genindex done highlighting module code... writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 9%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 22%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 35%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 48%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 57%] _images/pre_read_5mC.png copying images... [ 61%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 70%] _images/kmer_levels.png copying images... [ 74%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 83%] _images/begin_half_z_scores.png copying images... [ 87%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 96%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 5 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/reproducible-path/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/tombo-1.5.1/.pybuild/cpython3_3.12/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 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/_c_helper.cpython-312-aarch64-linux-gnu.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-aarch64-linux-gnu.so -> /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.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.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/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.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.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.5mC.model -> /build/reproducible-path/tombo-1.5.1/debian/tmp/usr/lib/python3.12/dist-packages/tombo/tombo_models 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/_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_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/__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/__main__.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/_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/_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/_option_parsers.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/_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/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/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/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/_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/_event_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/_plot_commands.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/__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/__main__.py to __main__.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/_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/_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/_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/_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/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/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/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/_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/_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/_plot_commands.py to _plot_commands.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-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.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_arm64.deb'. dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-7_all.deb'. dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-7_arm64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1999892/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1999892 and its subdirectories I: Current time: Thu Jan 22 14:51:02 +14 2026 I: pbuilder-time-stamp: 1769043062