Mon Jun 5 05:35:11 UTC 2023 I: starting to build tombo/bookworm/armhf on jenkins on '2023-06-05 05:34'
Mon Jun 5 05:35:11 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_11/1839/console.log
Mon Jun 5 05:35:11 UTC 2023 I: Downloading source for bookworm/tombo=1.5.1-4
--2023-06-05 05:35:11-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tombo/tombo_1.5.1-4.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2292 (2.2K) [text/prs.lines.tag]
Saving to: ‘tombo_1.5.1-4.dsc’
0K .. 100% 105M=0s
2023-06-05 05:35:12 (105 MB/s) - ‘tombo_1.5.1-4.dsc’ saved [2292/2292]
Mon Jun 5 05:35:12 UTC 2023 I: tombo_1.5.1-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: tombo
Binary: tombo, tombo-doc
Architecture: any all
Version: 1.5.1-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/nanoporetech/tombo
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/tombo
Vcs-Git: https://salsa.debian.org/med-team/tombo.git
Testsuite: autopkgtest
Build-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 <!nocheck>, python3-mappy <!nocheck>, python3-numpy <!nocheck>, python3-scipy <!nocheck>, python3-tqdm <!nocheck>, python3-nose2 <!nocheck>
Package-List:
tombo deb science optional arch=any
tombo-doc deb doc optional arch=all
Checksums-Sha1:
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a0c233a81dd497af34853fe1b2c83ec6425576fa 6468 tombo_1.5.1-4.debian.tar.xz
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ae312d3da913b7917e162c9f752bad5a7c997227dc9afd4af8497e18beba9b31 6468 tombo_1.5.1-4.debian.tar.xz
Files:
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6fb5990f86dd4fdf1a199c3f9a21ee9d 6468 tombo_1.5.1-4.debian.tar.xz
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Mon Jun 5 05:35:12 UTC 2023 I: Checking whether the package is not for us
Mon Jun 5 05:35:12 UTC 2023 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net.
Mon Jun 5 05:35:12 UTC 2023 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net.
Mon Jun 5 05:43:22 UTC 2023 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 4 17:35:23 -12 2023
I: pbuilder-time-stamp: 1685943323
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/7390/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='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='dc692fcd3d3844a4bc65e0484074f4d6'
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='7390'
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.sYs5cg6Y/pbuilderrc_XBS4 --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.sYs5cg6Y/b1 --logfile b1/build.log tombo_1.5.1-4.dsc'
SUDO_GID='112'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt32b 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/7390/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19324 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} 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} 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} 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-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-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-pygments{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, 125 newly installed, 0 to remove and 0 not upgraded.
Need to get 95.8 MB of archives. After unpacking 415 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf fonts-lato all 2.0-2.1 [2696 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B]
Get: 12 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf sgml-base all 1.31 [15.4 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.9-1 [1381 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 23 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf cython3 armhf 0.29.32-2+b1 [1230 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 37 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 38 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 39 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 40 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 44 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 47 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 48 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB]
Get: 49 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130 [104 kB]
Get: 50 http://deb.debian.org/debian bookworm/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get: 51 http://deb.debian.org/debian bookworm/main armhf docutils-common all 0.19+dfsg-6 [127 kB]
Get: 52 http://deb.debian.org/debian bookworm/main armhf docutils-doc all 0.19+dfsg-6 [1098 kB]
Get: 53 http://deb.debian.org/debian bookworm/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 54 http://deb.debian.org/debian bookworm/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get: 55 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB]
Get: 56 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB]
Get: 57 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB]
Get: 58 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB]
Get: 59 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB]
Get: 60 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB]
Get: 61 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB]
Get: 62 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB]
Get: 63 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB]
Get: 64 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB]
Get: 65 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-10 [347 kB]
Get: 66 http://deb.debian.org/debian bookworm/main armhf libexpat1-dev armhf 2.5.0-1 [134 kB]
Get: 67 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB]
Get: 68 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B]
Get: 69 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB]
Get: 70 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB]
Get: 71 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 72 http://deb.debian.org/debian bookworm/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get: 73 http://deb.debian.org/debian bookworm/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 74 http://deb.debian.org/debian bookworm/main armhf libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 75 http://deb.debian.org/debian bookworm/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get: 76 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB]
Get: 77 http://deb.debian.org/debian bookworm/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [25.0 kB]
Get: 78 http://deb.debian.org/debian bookworm/main armhf liblzf1 armhf 3.6-3 [9248 B]
Get: 79 http://deb.debian.org/debian bookworm/main armhf libpython3.11 armhf 3.11.2-6 [1710 kB]
Get: 80 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB]
Get: 81 http://deb.debian.org/debian bookworm/main armhf libpython3.11-dev armhf 3.11.2-6 [3518 kB]
Get: 82 http://deb.debian.org/debian bookworm/main armhf libpython3-dev armhf 3.11.2-1+b1 [9556 B]
Get: 83 http://deb.debian.org/debian bookworm/main armhf libpython3-all-dev armhf 3.11.2-1+b1 [1068 B]
Get: 84 http://deb.debian.org/debian bookworm/main armhf python-babel-localedata all 2.10.3-1 [5615 kB]
Get: 85 http://deb.debian.org/debian bookworm/main armhf python-requests-doc all 2.28.1+dfsg-1 [183 kB]
Get: 86 http://deb.debian.org/debian bookworm/main armhf python3-alabaster all 0.7.12-1 [20.8 kB]
Get: 87 http://deb.debian.org/debian bookworm/main armhf python3-all armhf 3.11.2-1+b1 [1060 B]
Get: 88 http://deb.debian.org/debian bookworm/main armhf python3.11-dev armhf 3.11.2-6 [615 kB]
Get: 89 http://deb.debian.org/debian bookworm/main armhf python3-dev armhf 3.11.2-1+b1 [26.2 kB]
Get: 90 http://deb.debian.org/debian bookworm/main armhf python3-all-dev armhf 3.11.2-1+b1 [1076 B]
Get: 91 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 92 http://deb.debian.org/debian bookworm/main armhf python3-tz all 2022.7.1-4 [30.1 kB]
Get: 93 http://deb.debian.org/debian bookworm/main armhf python3-babel all 2.10.3-1 [103 kB]
Get: 94 http://deb.debian.org/debian bookworm/main armhf python3-certifi all 2022.9.24-1 [153 kB]
Get: 95 http://deb.debian.org/debian bookworm/main armhf python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 96 http://deb.debian.org/debian bookworm/main armhf python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 97 http://deb.debian.org/debian bookworm/main armhf python3-decorator all 5.1.1-3 [14.9 kB]
Get: 98 http://deb.debian.org/debian bookworm/main armhf python3.11-doc all 3.11.2-6 [12.6 MB]
Get: 99 http://deb.debian.org/debian bookworm/main armhf python3-doc all 3.11.2-1 [9208 B]
Get: 100 http://deb.debian.org/debian bookworm/main armhf python3-roman all 3.3-3 [9880 B]
Get: 101 http://deb.debian.org/debian bookworm/main armhf python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 102 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB]
Get: 103 http://deb.debian.org/debian bookworm/main armhf python3-h5py-serial armhf 3.7.0-8 [730 kB]
Get: 104 http://deb.debian.org/debian bookworm/main armhf python3-h5py all 3.7.0-8 [10.3 kB]
Get: 105 http://deb.debian.org/debian bookworm/main armhf python3-idna all 3.3-1 [39.4 kB]
Get: 106 http://deb.debian.org/debian bookworm/main armhf python3-imagesize all 1.4.1-1 [6688 B]
Get: 107 http://deb.debian.org/debian bookworm/main armhf python3-markupsafe armhf 2.1.2-1+b1 [12.8 kB]
Get: 108 http://deb.debian.org/debian bookworm/main armhf python3-jinja2 all 3.1.2-1 [119 kB]
Get: 109 http://deb.debian.org/debian bookworm/main armhf python3-mappy armhf 2.24+dfsg-3+b1 [147 kB]
Get: 110 http://deb.debian.org/debian bookworm/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get: 111 http://deb.debian.org/debian bookworm/main armhf python3-nose2 all 0.12.0-1 [107 kB]
Get: 112 http://deb.debian.org/debian bookworm/main armhf python3-packaging all 23.0-1 [32.5 kB]
Get: 113 http://deb.debian.org/debian bookworm/main armhf python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get: 114 http://deb.debian.org/debian bookworm/main armhf python3-urllib3 all 1.26.12-1 [117 kB]
Get: 115 http://deb.debian.org/debian bookworm/main armhf python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 116 http://deb.debian.org/debian bookworm/main armhf python3-scipy armhf 1.10.1-2 [13.8 MB]
Get: 117 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB]
Get: 118 http://deb.debian.org/debian bookworm/main armhf python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get: 119 http://deb.debian.org/debian bookworm/main armhf sphinx-common all 5.3.0-4 [653 kB]
Get: 120 http://deb.debian.org/debian bookworm/main armhf python3-sphinx all 5.3.0-4 [549 kB]
Get: 121 http://deb.debian.org/debian bookworm/main armhf sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB]
Get: 122 http://deb.debian.org/debian bookworm/main armhf python3-sphinx-argparse all 0.3.2-1 [37.1 kB]
Get: 123 http://deb.debian.org/debian bookworm/main armhf python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB]
Get: 124 http://deb.debian.org/debian bookworm/main armhf python3-tqdm all 4.64.1-1 [97.7 kB]
Get: 125 http://deb.debian.org/debian bookworm/main armhf sphinx-doc all 5.3.0-4 [2307 kB]
Fetched 95.8 MB in 9s (10.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package fonts-lato.
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Selecting previously unselected package libpython3.11-minimal:armhf.
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ...
Unpacking libpython3.11-minimal:armhf (3.11.2-6) ...
Selecting previously unselected package libexpat1:armhf.
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Unpacking libexpat1:armhf (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:armhf (3.11.2-6) ...
Setting up libexpat1:armhf (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
Selecting previously unselected package python3-minimal.
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Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.deb ...
Unpacking python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.0.0_all.deb ...
Unpacking media-types (10.0.0) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
Unpacking readline-common (8.2-1.3) ...
Selecting previously unselected package libreadline8:armhf.
Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ...
Unpacking libreadline8:armhf (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:armhf.
Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ...
Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ...
Selecting previously unselected package python3.11.
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Unpacking python3.11 (3.11.2-6) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ...
Setting up python3-minimal (3.11.2-1+b1) ...
Selecting previously unselected package python3.
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Preparing to unpack .../000-python3_3.11.2-1+b1_armhf.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.
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Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package openssl.
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Unpacking openssl (3.0.9-1) ...
Selecting previously unselected package ca-certificates.
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Unpacking ca-certificates (20230311) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:armhf.
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Unpacking libmagic1:armhf (1:5.44-3) ...
Selecting previously unselected package file.
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Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../008-gettext-base_0.21-12_armhf.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../009-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../010-groff-base_1.22.4-10_armhf.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
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Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:armhf.
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Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
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Preparing to unpack .../014-m4_1.4.19-3_armhf.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
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Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
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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.
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Unpacking autopoint (0.21-12) ...
Selecting previously unselected package cython3.
Preparing to unpack .../019-cython3_0.29.32-2+b1_armhf.deb ...
Unpacking cython3 (0.29.32-2+b1) ...
Selecting previously unselected package libdebhelper-perl.
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Unpacking libdebhelper-perl (13.11.4) ...
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Unpacking libarchive-zip-perl (1.68-1) ...
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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.
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Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
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Unpacking libelf1:armhf (0.188-2.1) ...
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Unpacking dwz (0.15-1) ...
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Unpacking libicu72:armhf (72.1-3) ...
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Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
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Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
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Unpacking intltool-debian (0.35.0+20060710.6) ...
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Unpacking po-debconf (1.0.21+nmu1) ...
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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.
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Unpacking python3-distutils (3.11.2-3) ...
Selecting previously unselected package dh-python.
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Unpacking dh-python (5.20230130) ...
Selecting previously unselected package xml-core.
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Unpacking xml-core (0.18+nmu1) ...
Selecting previously unselected package docutils-common.
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Unpacking docutils-common (0.19+dfsg-6) ...
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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:armhf.
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
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done.
Reading package lists...
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-> 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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base: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-armhf' 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_helper.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/tombo_stats.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/_preprocess.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
copying tombo/_plot_commands.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/resquiggle.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
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
/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)
cythoning tombo/_c_helper.pyx to tombo/_c_helper.cpp
/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)
building 'tombo._c_dynamic_programming' extension
creating build
creating build/temp.linux-armhf-cpython-311
creating build/temp.linux-armhf-cpython-311/tombo
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tombo/_c_dynamic_programming.cpp -o build/temp.linux-armhf-cpython-311/tombo/_c_dynamic_programming.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
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:760:
/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 " \
| ^~~~~~~
tombo/_c_dynamic_programming.cpp: In function 'PyObject* __pyx_pf_5tombo_22_c_dynamic_programming_2c_reg_z_scores(PyObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, PyArrayObject*, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_INT_t, PyObject*)':
tombo/_c_dynamic_programming.cpp:3782:36: warning: '__pyx_v_np_max_half_z_score' may be used uninitialized [-Wmaybe-uninitialized]
3782 | __pyx_t_20 = PyFloat_FromDouble(__pyx_v_np_max_half_z_score); if (unlikely(!__pyx_t_20)) __PYX_ERR(0, 93, __pyx_L1_error)
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tombo/_c_dynamic_programming.cpp:2991:51: note: '__pyx_v_np_max_half_z_score' was declared here
2991 | __pyx_t_5tombo_22_c_dynamic_programming_DTYPE_t __pyx_v_np_max_half_z_score;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/tombo/_c_dynamic_programming.o -L/usr/lib/arm-linux-gnueabihf -o /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.cpython-311-arm-linux-gnueabihf.so
building 'tombo._c_helper' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tombo/_c_helper.cpp -o build/temp.linux-armhf-cpython-311/tombo/_c_helper.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
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:760:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tombo-1.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/tombo/_c_helper.o -L/usr/lib/arm-linux-gnueabihf -o /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_helper.cpython-311-arm-linux-gnueabihf.so
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/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/_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/tombo_stats.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/_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/_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/_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/_c_helper.cpython-311-arm-linux-gnueabihf.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/__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/__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/_c_helper.pyx -> /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.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.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.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.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.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.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.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
copying /build/tombo-1.5.1/.pybuild/cpython3_3.11/build/tombo/_c_dynamic_programming.cpython-311-arm-linux-gnueabihf.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/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/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/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/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/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/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/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/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/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/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/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/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/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/_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/_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/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/_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/_default_parameters.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/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/_version.py to _version.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
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/_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/_preprocess.py to _preprocess.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/__init__.py to __init__.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/_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/resquiggle.py to resquiggle.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/_default_parameters.py to _default_parameters.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_armhf.deb'.
dpkg-deb: building package 'tombo-dbgsym' in '../tombo-dbgsym_1.5.1-4_armhf.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_armhf.buildinfo
dpkg-genchanges --build=binary -O../tombo_1.5.1-4_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/7390 and its subdirectories
I: Current time: Sun Jun 4 17:40:15 -12 2023
I: pbuilder-time-stamp: 1685943615
Mon Jun 5 05:43:27 UTC 2023 I: 1st build successful. Starting 2nd build on remote node jtx1c-armhf-rb.debian.net.
Mon Jun 5 05:43:27 UTC 2023 I: Preparing to do remote build '2' on jtx1c-armhf-rb.debian.net.
Mon Jun 5 05:49:10 UTC 2023 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net.
Mon Jun 5 05:49:13 UTC 2023 I: tombo_1.5.1-4_armhf.changes:
Format: 1.8
Date: Tue, 29 Nov 2022 20:49:19 +0100
Source: tombo
Binary: tombo tombo-dbgsym tombo-doc
Architecture: armhf all
Version: 1.5.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
tombo - identification of modified nucleotides from raw nanopore sequenci
tombo-doc - identification of modified nucleotides from raw nanopore sequenci
Changes:
tombo (1.5.1-4) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
Checksums-Sha1:
a848cf64c3a270da86105c85da6ed494322e6e69 385496 tombo-dbgsym_1.5.1-4_armhf.deb
71774d7fcd103613b8960d28b958cfb5d25e0e3c 21732224 tombo-doc_1.5.1-4_all.deb
f260e628cb8f67ef68e061bc18d64047197a1b3a 8453 tombo_1.5.1-4_armhf.buildinfo
b552aac9c7c3ceb924f539a2c6e974f436ab10f0 421988 tombo_1.5.1-4_armhf.deb
Checksums-Sha256:
895a6b7343f62f691f3b173f2343bb35a18ed1b95f6cdc41026ff3715e841460 385496 tombo-dbgsym_1.5.1-4_armhf.deb
e368449d1ab51942f1c099b0a6b8d5c7c51c031ee6214226f4ae188f1f61043a 21732224 tombo-doc_1.5.1-4_all.deb
6e628f83b8c6ebf4abd42c384adc7abe415f16e83d7fb918ba25706fc52af5c3 8453 tombo_1.5.1-4_armhf.buildinfo
294d84cc44023088ae66837671b292fbc1af0d33bf951cead1a6425f8a260bbd 421988 tombo_1.5.1-4_armhf.deb
Files:
bd4a2ec6dbf3e2167d04ac9a7e0369de 385496 debug optional tombo-dbgsym_1.5.1-4_armhf.deb
0388628dccc0dd1ee91090056b760dce 21732224 doc optional tombo-doc_1.5.1-4_all.deb
dd5299bbb736607f6ed577cddf809293 8453 science optional tombo_1.5.1-4_armhf.buildinfo
8165455b0c8cf4cae1e1ca247148780a 421988 science optional tombo_1.5.1-4_armhf.deb
Mon Jun 5 05:49:14 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sYs5cg6Y/tombo_1.5.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sYs5cg6Y/tombo_1.5.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sYs5cg6Y/tombo_1.5.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sYs5cg6Y/b1/tombo_1.5.1-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.sYs5cg6Y/b2/tombo_1.5.1-4_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.542s)
0.541s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.248s)
0.247s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Mon Jun 5 05:49:15 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Mon Jun 5 05:49:15 UTC 2023 I: tombo from bookworm built successfully and reproducibly on armhf.
Mon Jun 5 05:49:16 UTC 2023 I: Submitting .buildinfo files to external archives:
Mon Jun 5 05:49:16 UTC 2023 I: Submitting 12K b1/tombo_1.5.1-4_armhf.buildinfo.asc
Mon Jun 5 05:49:18 UTC 2023 I: Submitting 12K b2/tombo_1.5.1-4_armhf.buildinfo.asc
Mon Jun 5 05:49:19 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Jun 5 05:49:19 UTC 2023 I: Done submitting .buildinfo files.
Mon Jun 5 05:49:19 UTC 2023 I: Removing signed tombo_1.5.1-4_armhf.buildinfo.asc files:
removed './b1/tombo_1.5.1-4_armhf.buildinfo.asc'
removed './b2/tombo_1.5.1-4_armhf.buildinfo.asc'