I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 4 17:29:46 -12 2023
I: pbuilder-time-stamp: 1685942986
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 [ctdopts_1.5-2.dsc]
I: copying [./ctdopts_1.5.orig.tar.gz]
I: copying [./ctdopts_1.5-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Nov 2 22:44:34 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 ./ctdopts_1.5-2.dsc: no acceptable signature found
dpkg-source: info: extracting ctdopts in ctdopts-1.5
dpkg-source: info: unpacking ctdopts_1.5.orig.tar.gz
dpkg-source: info: unpacking ctdopts_1.5-2.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2720658/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=15 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='044362bfe297467f9f8cddb5f230dd51'
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='2720658'
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.JsXeBiVE/pbuilderrc_Jstr --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.JsXeBiVE/b1 --logfile b1/build.log ctdopts_1.5-2.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 09:23 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 01:20 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 22:02 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 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount
-rwxr-xr-x 1 root root 203152 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 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 00:40 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 22:02 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 22:02 more
-rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount
-rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint
-rwxr-xr-x 1 root root 142968 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 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:23 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 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 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 22:02 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 02:25 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 20:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 22:02 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 22:02 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/2720658/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 <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, python3-setuptools, 2to3, python3-tz
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19591 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; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on 2to3; however:
Package 2to3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-tz; however:
Package python3-tz 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:
2to3{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3-tz{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.6 MB of archives. After unpacking 100 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 2to3 all 3.11.2-1 [10.0 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB]
Fetched 25.6 MB in 1s (42.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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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.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (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_amd64.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 ...
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Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ...
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) ...
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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) ...
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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.
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Unpacking python3 (3.11.2-1+b1) ...
Selecting previously unselected package sensible-utils.
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Unpacking gettext-base (0.21-12) ...
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Unpacking libuchardet0:amd64 (0.0.7-1) ...
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I: Building the package
I: Running cd /build/ctdopts-1.5/ && 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 > ../ctdopts_1.5-2_source.changes
dpkg-buildpackage: info: source package ctdopts
dpkg-buildpackage: info: source version 1.5-2
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 amd64
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py clean
'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
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dh binary --with python3 --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
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/ctdopts-1.5'
dh_auto_build
I: pybuild base:240: /usr/bin/python3 setup.py build
# an override, not a PYBUILD directive, as we only need to do this once
# not for every Python version
2to3 --write --nobackups --no-diffs --output-dir=debian example.py
/usr/bin/2to3:3: DeprecationWarning: lib2to3 package is deprecated and may not be able to parse Python 3.10+
from lib2to3.main import main
lib2to3.main: Output in 'debian' will mirror the input directory '' layout.
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored example.py
RefactoringTool: Writing converted example.py to debian/example.py.
RefactoringTool: Files that were modified:
RefactoringTool: example.py
make[1]: Leaving directory '/build/ctdopts-1.5'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/ctdopts-1.5'
export PYBUILD_SYSTEM=custom; dh_auto_test
I: pybuild base:240: PYTHONPATH=/build/ctdopts-1.5/.pybuild/cpython3_3.11_CTDopts/build python3.11 debian/example.py
/build/ctdopts-1.5/.pybuild/cpython3_3.11_CTDopts/build/CTDopts/CTDopts.py:1071: UserWarning: Argument restrictions for positive_int violated. Restriction: 0:. Value: -5
warnings.warn('Argument restrictions for %s violated. Restriction: %s. Value: %s' %
/build/ctdopts-1.5/.pybuild/cpython3_3.11_CTDopts/build/CTDopts/CTDopts.py:1071: UserWarning: Argument restrictions for output violated. Restriction: *.fastq,*.fastq.gz. Value:
warnings.warn('Argument restrictions for %s violated. Restriction: %s. Value: %s' %
Model being written to exampleTool.ctd...
Model loaded from exampleTool.ctd...
For debugging purposes we can output a human readable representation of Parameter objects. Here's the first one:
PARAMETER positive_int
type: int
default: 5
tags: advanced, magic
restrictions on numeric range: 0 to None
description: A positive integer parameter
The following parameters were registered in the model:
['positive_int', 'input_files', 'output', 'this_that', 'param_1', 'param_2', 'param_3']
The same parameters with subgroup information, if they were registered under parameter groups:
['positive_int', 'input_files', 'output', 'this_that', 'subparams:param_1', 'subparams:param_2', 'subparams:subsubparam:param_3']
A dictionary of parameters with default values, returned by CTDModel.get_defaults():
{ 'positive_int': 5,
'subparams': { 'param_1': 5.5,
'param_2': [0.0, 2.5, 5.0],
'subsubparam': {'param_3': 2}},
'this_that': 'this'}
As you can see, parameter values are usually stored in nested dictionaries. If you want a flat dictionary, you canget that using CTDopts.flatten_dict(). Flat keys can be either tuples of tree node (subgroup) names down to the parameter...
{ ('positive_int',): 5,
('subparams', 'param_1'): 5.5,
('subparams', 'param_2'): [0.0, 2.5, 5.0],
('subparams', 'subsubparam', 'param_3'): 2,
('this_that',): 'this'}
...or they can be strings where nesing levels are separated by colons:
{ 'positive_int': 5,
'subparams:param_1': 5.5,
'subparams:param_2': [0.0, 2.5, 5.0],
'subparams:subsubparam:param_3': 2,
'this_that': 'this'}
We can create dictionaries of arguments on our own that we want to validate against the model.CTDopts can read them from argument-storing CTD files or from the command line, but we can just define them in a nested dictionary on our own as well. We start with defining them explicitly.
{ 'input_files': ['file1.fastq', 'file2.fastq', 'file3.fastq'],
'positive_int': 111,
'subparams': {'param_1': '999.0'}}
We can validate these arguments against the model, and get a dictionary with parameter types correctly casted and defaults set. Note that subparams:param_1 was casted from string to a floating point number because that's how it was defined in the model.
{ 'input_files': ['file1.fastq', 'file2.fastq', 'file3.fastq'],
'positive_int': 111,
'subparams': { 'param_1': 999.0,
'param_2': [0.0, 2.5, 5.0],
'subsubparam': {'param_3': 2}},
'this_that': 'this'}
We can write a CTD file containing these validated argument values. Just call CTDModel.write_ctd() with an extra parameter: the nested argument dictionary containing the actual values.
As mentioned earlier, CTDopts can load argument values from CTD files. Feel free to change some values in exampleTool_preset_params.ctd you've just written, and load it back.
{ 'input_files': ['file1.fastq', 'file2.fastq', 'file3.fastq'],
'output': '',
'positive_int': '111',
'subparams': { 'param_1': '999.0',
'param_2': ['0.0', '2.5', '5.0'],
'subsubparam': {'param_3': '2'}},
'this_that': 'this'}
Notice that all the argument values are strings now. This is because we didn't validate them against the model, just loaded some stuff from a file into a dictionary. If you want to cast them, call CTDModel.validate_args():
{ 'input_files': ['file1.fastq', 'file2.fastq', 'file3.fastq'],
'output': '',
'positive_int': 111,
'subparams': { 'param_1': 999.0,
'param_2': [0.0, 2.5, 5.0],
'subsubparam': {'param_3': 2}},
'this_that': 'this'}
Now certain parameters may have restrictions that we might want to validate for as well. Let's set the parameter positive_int to a negative value, and try to validate it with a strictness level enforce_restrictions=1. This will register a warning, but still accept the value.
Validation enforcement levels can be 0, 1 or 2 for type-casting, restriction-checking and required argument presence. They can be set with the keywords enforce_type, enforce_restrictions and enforce_required respectively. Let's increase strictness for restriction checking. CTDModel.validate_args() will now raise an exception that we'll catch:
Argument restrictions for positive_int failed. Restriction: 0:. Value: -5
One might want to combine arguments loaded from a CTD file with arguments coming from elsewhere, like the command line.In that case, the method CTDopts.override_args(*arg_dicts) creates a combined argument dictionary where argument values are always taken from the rightmost (last) dictionary that has them. Let's override a few parameters:
{ 'input_files': ['file1.fastq', 'file2.fastq', 'file3.fastq'],
'positive_int': 777,
'subparams': { 'param_1': 999.0,
'param_2': [0.0, 2.5, 5.0],
'subsubparam': {'param_3': 2}},
'this_that': 'that'}
So how to deal with command line arguments? If we have a model, we can look for its arguments. Call CTDModel.parse_cl_args() with either a string of the command line call or a list with the split words. By default, it will assume a '--' prefix before parameter names, but it can be overridden with prefix='-'.Grouped parameters are expected in --group:subgroup:param_x format.
{ 'input_files': ['a.fastq', 'b.fastq'],
'output': 'out_dir/',
'positive_int': '44',
'subparams': { 'param_1': 5.5,
'param_2': ['5.0', '5.5', '6.0'],
'subsubparam': {'param_3': 2}},
'this_that': 'this'}
Override other parameters with them, and validate it against the model:
{ 'input_files': ['a.fastq', 'b.fastq'],
'output': 'out_dir/',
'positive_int': 44,
'subparams': { 'param_1': 5.5,
'param_2': [5.0, 5.5, 6.0],
'subsubparam': {'param_3': 2}},
'this_that': 'this'}
One last thing: certain command line directives that are specific to CTD functionality can be parsed for, to help your script performing common tasks. These are CTD argument input, CTD model file writing and CTD argument file writing. CTDopts.parse_cl_directives() can also be customized as to what directives to look for if the defaults --input_ctd, --write_tool_ctd and --write_param_ctd respectively don't satisfy you.
{ 'input_ctd': 'exampleTool_preset_params.ctd',
'write_param_ctd': 'new_preset_params.ctd',
'write_tool_ctd': None}
{ 'input_ctd': 'exampleTool_preset_params_2.ctd',
'write_param_ctd': None,
'write_tool_ctd': True}
Finally, writing CTDs with logging information, passing a dictionarywith a 'log' keyword, using any or all of the fields shown below.
make[1]: Leaving directory '/build/ctdopts-1.5'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install --destdir=debian/python3-ctdopts/ -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/ctdopts-1.5/debian/python3-ctdopts
/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(
dh_install -O--buildsystem=pybuild
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
dh_installexamples -O--buildsystem=pybuild
dh_python3 -O--buildsystem=pybuild
dh_installsystemduser -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
dh_link -O--buildsystem=pybuild
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dh_compress -O--buildsystem=pybuild
dh_fixperms -O--buildsystem=pybuild
dh_missing -O--buildsystem=pybuild
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dh_gencontrol -O--buildsystem=pybuild
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'python3-ctdopts' in '../python3-ctdopts_1.5-2_all.deb'.
dpkg-genbuildinfo --build=binary -O../ctdopts_1.5-2_amd64.buildinfo
dpkg-genchanges --build=binary -O../ctdopts_1.5-2_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/2720658 and its subdirectories
I: Current time: Sun Jun 4 17:31:01 -12 2023
I: pbuilder-time-stamp: 1685943061