I: pbuilder: network access will be disabled during build I: Current time: Fri Jun 21 04:05:43 -12 2024 I: pbuilder-time-stamp: 1718985943 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.5.1-4.dsc] I: copying [./tombo_1.5.1.orig.tar.gz] I: copying [./tombo_1.5.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 29 07:53:23 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tombo_1.5.1-4.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_1.5.1-4.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2667488/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4127b4b6f7804a089c3654e127b4f4f3' 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='2667488' 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.l4hlSPvq/pbuilderrc_WGO4 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l4hlSPvq/b1 --logfile b1/build.log tombo_1.5.1-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2667488/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-sphinx-argparse, libjs-mathjax, python3-h5py, python3-mappy, python3-numpy, python3-scipy, python3-tqdm, python3-nose2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on sphinx-doc; however: Package sphinx-doc is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx 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-sphinx-argparse; however: Package python3-sphinx-argparse is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax 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-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-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-nose2; however: Package python3-nose2 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} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-hl-100{a} libicu72{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} libldap-2.5-0{a} liblzf1{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} libxsimd-dev{a} m4{a} man-db{a} media-types{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-babel{a} python3-beniget{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-doc{a} python3-docutils{a} python3-gast{a} python3-h5py{a} python3-h5py-serial{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-mappy{a} python3-markupsafe{a} python3-minimal{a} python3-nose2{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-ply{a} python3-pygments{a} python3-pythran{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-argparse{a} python3-sphinx-rtd-theme{a} python3-tqdm{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-dev{a} python3.11-doc{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx publicsuffix python3-pil wget 0 packages upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 124 MB of archives. After unpacking 715 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 12 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 cython3 amd64 0.29.32-2+b1 [1302 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 docutils-doc all 0.19+dfsg-6 [1098 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 liblzf1 amd64 3.6-3 [10.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 python-requests-doc all 2.28.1+dfsg-1 [183 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 95 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 98 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 102 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 103 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 python3.11-doc all 3.11.2-6 [12.6 MB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 python3-doc all 3.11.2-1 [9208 B] Get: 109 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 110 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 python3-h5py-serial amd64 3.7.0-8 [804 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 python3-h5py all 3.7.0-8 [10.3 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 116 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 python3-mappy amd64 2.24+dfsg-3+b1 [133 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 python3-nose2 all 0.12.0-1 [107 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-argparse all 0.3.2-1 [37.1 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 sphinx-doc all 5.3.0-4 [2307 kB] Fetched 124 MB in 2s (81.1 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 ... 19596 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. 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Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20372 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-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 .../018-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package cython3. Preparing to unpack .../019-cython3_0.29.32-2+b1_amd64.deb ... Unpacking cython3 (0.29.32-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../020-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../021-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../022-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../023-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../024-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../025-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../026-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../027-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../028-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../029-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../030-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../031-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../032-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../033-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../034-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../035-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../036-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../037-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package xml-core. Preparing to unpack .../038-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../039-docutils-common_0.19+dfsg-6_all.deb ... Unpacking docutils-common (0.19+dfsg-6) ... Selecting previously unselected package docutils-doc. Preparing to unpack .../040-docutils-doc_0.19+dfsg-6_all.deb ... Unpacking docutils-doc (0.19+dfsg-6) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../041-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../042-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../043-libaec0_1.0.6-1+b1_amd64.deb ... Unpacking libaec0:amd64 (1.0.6-1+b1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../044-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../045-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../046-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../047-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../048-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../049-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../050-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../051-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../052-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../053-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../054-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../055-libcurl4_7.88.1-9_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-9) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../056-libexpat1-dev_2.5.0-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.5.0-1) ... 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Selecting previously unselected package python3-doc. Preparing to unpack .../096-python3-doc_3.11.2-1_all.deb ... Unpacking python3-doc (3.11.2-1) ... Selecting previously unselected package python3-roman. Preparing to unpack .../097-python3-roman_3.3-3_all.deb ... Unpacking python3-roman (3.3-3) ... Selecting previously unselected package python3-docutils. Preparing to unpack .../098-python3-docutils_0.19+dfsg-6_all.deb ... Unpacking python3-docutils (0.19+dfsg-6) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../099-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-h5py-serial. Preparing to unpack .../100-python3-h5py-serial_3.7.0-8_amd64.deb ... Unpacking python3-h5py-serial (3.7.0-8) ... Selecting previously unselected package python3-h5py. Preparing to unpack .../101-python3-h5py_3.7.0-8_all.deb ... Unpacking python3-h5py (3.7.0-8) ... Selecting previously unselected package python3-idna. Preparing to unpack .../102-python3-idna_3.3-1_all.deb ... Unpacking python3-idna (3.3-1) ... Selecting previously unselected package python3-imagesize. Preparing to unpack .../103-python3-imagesize_1.4.1-1_all.deb ... Unpacking python3-imagesize (1.4.1-1) ... Selecting previously unselected package python3-markupsafe. Preparing to unpack .../104-python3-markupsafe_2.1.2-1+b1_amd64.deb ... Unpacking python3-markupsafe (2.1.2-1+b1) ... Selecting previously unselected package python3-jinja2. Preparing to unpack .../105-python3-jinja2_3.1.2-1_all.deb ... Unpacking python3-jinja2 (3.1.2-1) ... Selecting previously unselected package python3-mappy. Preparing to unpack .../106-python3-mappy_2.24+dfsg-3+b1_amd64.deb ... Unpacking python3-mappy (2.24+dfsg-3+b1) ... Selecting previously unselected package python3-six. Preparing to unpack .../107-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... 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Unpacking python3-sphinx (5.3.0-4) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../120-sphinx-rtd-theme-common_1.2.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Selecting previously unselected package python3-sphinx-argparse. Preparing to unpack .../121-python3-sphinx-argparse_0.3.2-1_all.deb ... Unpacking python3-sphinx-argparse (0.3.2-1) ... Selecting previously unselected package python3-sphinx-rtd-theme. Preparing to unpack .../122-python3-sphinx-rtd-theme_1.2.0+dfsg-1_all.deb ... Unpacking python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../123-python3-tqdm_4.64.1-1_all.deb ... Unpacking python3-tqdm (4.64.1-1) ... Selecting previously unselected package sphinx-doc. Preparing to unpack .../124-sphinx-doc_5.3.0-4_all.deb ... Unpacking sphinx-doc (5.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up fonts-lato (2.0-2.1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up docutils-doc (0.19+dfsg-6) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up liblzf1:amd64 (3.6-3) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.0.8-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libsz2:amd64 (1.0.6-1+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 (1.13.1-1) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up python3.11-doc (3.11.2-6) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up python-requests-doc (2.28.1+dfsg-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:amd64 (7.88.1-9) ... Setting up python3-doc (3.11.2-1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up sphinx-doc (5.3.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up sphinx-common (5.3.0-4) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-ply (3.11-5) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-mappy (2.24+dfsg-3+b1) ... Setting up python3-nose2 (0.12.0-1) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-h5py-serial (3.7.0-8) ... Setting up python3-h5py (3.7.0-8) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Setting up python3-sphinx-argparse (0.3.2-1) ... Processing triggers for ca-certificates (20230311) ... 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/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_1.5.1-4_source.changes dpkg-buildpackage: info: source package tombo dpkg-buildpackage: info: source version 1.5.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/tombo-1.5.1/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it 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:240: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/tombo-1.5.1' dh_auto_build I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/tombo_stats.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/tombo_helper.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/resquiggle.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_version.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_text_output_commands.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_preprocess.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_plot_commands.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_option_parsers.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_filter_reads.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_event_resquiggle.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_default_parameters.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/__main__.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/__init__.py -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/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:202: SetuptoolsDeprecationWarning: Installing 'tombo.R_scripts' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'tombo.R_scripts' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'tombo.R_scripts' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'tombo.tombo_models' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'tombo.tombo_models' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'tombo.tombo_models' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying tombo/_c_dynamic_programming.pyx -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo copying tombo/_c_helper.pyx -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo creating /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugDP.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugFit.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/debugRawDP.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotGroupComp.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotKmerDist.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotModelComp.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotMotifStats.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotMultiReadCorr.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotPerReadStats.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotROC.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotROCPerRead.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotReadCorr.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSigMDS.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRead.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts copying tombo/R_scripts/plotSingleRun.R -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts creating /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.5mC.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.6mA.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.CpG.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dam.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.dcm.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.DNA.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.180mV.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.200mV.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models copying tombo/tombo_models/tombo.RNA.5mC.model -> /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models running build_ext cythoning tombo/_c_dynamic_programming.pyx to tombo/_c_dynamic_programming.cpp INFO: Disabling color, you really want to install colorlog. Disabling color, you really want to install colorlog. /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar. if not hasattr(numpy, method): /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar. obj = getattr(themodule, elem) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tombo-1.5.1/tombo/_c_dynamic_programming.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tombo-1.5.1/tombo/_c_helper.pyx tree = Parsing.p_module(s, pxd, full_module_name) sphinx-build -N -bhtml docs docs/build Running Sphinx v5.3.0 Creating file ./tombo.rst. making output directory... done building [mo]: targets for 0 po files that are out of date 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... [ 54%] plotting reading sources... [ 63%] resquiggle reading sources... [ 72%] rna reading sources... [ 81%] text_output reading sources... [ 90%] 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 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... [ 54%] plotting writing output... [ 63%] resquiggle writing output... [ 72%] rna writing output... [ 81%] text_output writing output... [ 90%] tombo writing output... [100%] tutorials generating indices... genindex done writing additional pages... search done copying images... [ 4%] _images/testing_method_comparison.png copying images... [ 8%] _images/alt_density_est.png copying images... [ 13%] _images/old_correction_plot.png copying images... [ 17%] _images/outlier_robust_llr.gif copying images... [ 21%] _images/dampened_fraction.png copying images... [ 26%] _images/single_samp.png copying images... [ 30%] _images/sample_comp.png copying images... [ 34%] _images/model_comp.png copying images... [ 39%] _images/alt_model_comp.png copying images... [ 43%] _images/boxplot.png copying images... [ 47%] _images/quantile.png copying images... [ 52%] _images/density.png copying images... [ 56%] _images/pre_read_5mC.png copying images... [ 60%] _images/per_read_do_novo.png copying images... [ 65%] _images/stat_dist.png copying images... [ 69%] _images/kmer_levels.png copying images... [ 73%] _images/roc.png copying images... [ 78%] _images/per_read_stat_dist.png copying images... [ 82%] _images/begin_half_z_scores.png copying images... [ 86%] _images/begin_forward_pass.png copying images... [ 91%] _images/adaptive_half_z_scores.png copying images... [ 95%] _images/adaptive_forward_pass.png copying images... [100%] _images/stat_dist_null.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 4 warnings. The HTML pages are in docs/build. make[1]: Leaving directory '/build/tombo-1.5.1' dh_auto_test -O--buildsystem=pybuild I: pybuild base:240: cd /build/tombo-1.5.1/.pybuild/cpython3_3.11/build; python3.11 -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:240: /usr/bin/python3 setup.py install --root /build/tombo-1.5.1/debian/tmp running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( 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:202: SetuptoolsDeprecationWarning: Installing 'tombo.R_scripts' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'tombo.R_scripts' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'tombo.R_scripts' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'tombo.R_scripts' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'tombo.tombo_models' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'tombo.tombo_models' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'tombo.tombo_models' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'tombo.tombo_models' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running build_ext skipping 'tombo/_c_dynamic_programming.cpp' Cython extension (up-to-date) skipping 'tombo/_c_helper.cpp' Cython extension (up-to-date) running install_lib creating /build/tombo-1.5.1/debian/tmp/usr creating /build/tombo-1.5.1/debian/tmp/usr/lib creating /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11 creating /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages creating /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.cpython-311-x86_64-linux-gnu.so -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.cpython-311-x86_64-linux-gnu.so -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo creating /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.5mC.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.200mV.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.RNA.180mV.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.dcm.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.dam.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.CpG.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.6mA.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_models/tombo.DNA.5mC.model -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_models creating /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSingleRun.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSingleRead.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotSigMDS.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotReadCorr.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotROCPerRead.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotROC.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotPerReadStats.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotMultiReadCorr.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotMotifStats.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotModelComp.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotKmerDist.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/plotGroupComp.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugRawDP.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugFit.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/R_scripts/debugDP.R -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/R_scripts copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.pyx -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.pyx -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/__init__.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/__main__.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_default_parameters.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_event_resquiggle.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_filter_reads.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_option_parsers.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_plot_commands.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_preprocess.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_text_output_commands.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_version.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/resquiggle.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_helper.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/tombo_stats.py -> /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/__init__.py to __init__.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/__main__.py to __main__.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_default_parameters.py to _default_parameters.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_event_resquiggle.py to _event_resquiggle.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_filter_reads.py to _filter_reads.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_option_parsers.py to _option_parsers.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_plot_commands.py to _plot_commands.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_preprocess.py to _preprocess.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_text_output_commands.py to _text_output_commands.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/_version.py to _version.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/resquiggle.py to resquiggle.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_helper.py to tombo_helper.cpython-311.pyc byte-compiling /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/tombo/tombo_stats.py to tombo_stats.cpython-311.pyc running install_egg_info Copying ont_tombo.egg-info to /build/tombo-1.5.1/debian/tmp/usr/lib/python3.11/dist-packages/ont_tombo-1.5.1.egg-info Skipping SOURCES.txt running install_scripts Installing tombo script to /build/tombo-1.5.1/debian/tmp/usr/bin dh_install -O--buildsystem=pybuild 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:114: replacing shebang in debian/tombo/usr/share/tombo/scripts/dump_per_read_statistics.py 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 debian/rules override_dh_fixperms make[1]: Entering directory '/build/tombo-1.5.1' dh_fixperms find debian -name "*.model" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/tombo-1.5.1' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package tombo-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'tombo' in '../tombo_1.5.1-4_amd64.deb'. dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-4_amd64.deb'. dpkg-deb: building package 'tombo-doc' in '../tombo-doc_1.5.1-4_all.deb'. dpkg-genbuildinfo --build=binary -O../tombo_1.5.1-4_amd64.buildinfo dpkg-genchanges --build=binary -O../tombo_1.5.1-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2667488 and its subdirectories I: Current time: Fri Jun 21 04:08:29 -12 2024 I: pbuilder-time-stamp: 1718986109