Mon Jun 5 05:29:43 UTC 2023 I: starting to build ctdopts/bookworm/amd64 on jenkins on '2023-06-05 05:29' Mon Jun 5 05:29:43 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/242/console.log Mon Jun 5 05:29:43 UTC 2023 I: Downloading source for bookworm/ctdopts=1.5-2 --2023-06-05 05:29:43-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/ctdopts/ctdopts_1.5-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2058 (2.0K) [text/prs.lines.tag] Saving to: ‘ctdopts_1.5-2.dsc’ 0K .. 100% 165M=0s 2023-06-05 05:29:43 (165 MB/s) - ‘ctdopts_1.5-2.dsc’ saved [2058/2058] Mon Jun 5 05:29:43 UTC 2023 I: ctdopts_1.5-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ctdopts Binary: python3-ctdopts Architecture: all Version: 1.5-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/WorkflowConversion/CTDopts Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/ctdopts Vcs-Git: https://salsa.debian.org/med-team/ctdopts.git Testsuite: autopkgtest Testsuite-Triggers: 2to3, python3-all Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, 2to3, python3-tz Package-List: python3-ctdopts deb python optional arch=all Checksums-Sha1: 0c5263f3bf3f4005a98695e873859c647a58a727 34895 ctdopts_1.5.orig.tar.gz c342e5d9ca1a5eca3f8008225e8c5d4ad2122d98 3032 ctdopts_1.5-2.debian.tar.xz Checksums-Sha256: 0162fc066555f8f82dbb47a285393c58c864b1fcf549eacabba9e16b2dec9f73 34895 ctdopts_1.5.orig.tar.gz 8b74c7c41575706548124670f2ee8c3375b88aa5f0a1f94fc3d115322f0a338a 3032 ctdopts_1.5-2.debian.tar.xz Files: d17d2d548bf95c20abf81bb957d4fa5b 34895 ctdopts_1.5.orig.tar.gz 791b3ec3d9e30b939878983e4dbce127 3032 ctdopts_1.5-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNjm5IRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG3Gg/+MES4y6OGWOcV0kthtO17gHcric9qTbJm xbUXtu4bSpz/fqaibd+t8kz6eurJuchq6TART8cvyQ/HYR5OqBzky1vD+bK8iSZN dIhjBDfE/CGNsEjqPyu+Mh1SrKvXXISH6CI3f59MYshl8qAa8vcGPX9SeNL+/8vf bXnopzoeVly1D9xK2fBPM8XQ/G0uh0bb/komBYFY2mdbjzGi4hrycTKJQA9scFaD cnvYoLvYgktOduHNYgQh0k0Of3XUNQNThbNnWs4H0ww/E9iuIiyvY72Wjf8bj9pz iNAgWF+DrIGYFBsXQwpTgn3nPq2buBkOt1v87fdLm11Le6QpKI/cUHlrbI5cwsMA OwSRfH+abzbzFEiW9t1WbRCyBYOVSU9eHxrk4mGf78tcFGv2FxSq8+vOJGwSaMQS a2e5pHksgz9tFSc6sArcIioe2+F/1F1zZgPvtwdBjMOsbBzZLow4W+a0N2KtYAop p5DqeyGhVWbd9/gZEbORfRJFG4Wz5bIuS6stKNamcx57Iec4DA/t/pqcnYiMguZt j/Z2zMuE0wM2NE3yoSve8m8Y2520GQ9/8LYUWWqIvQ6+/9z06mF2r0b9k6B+n1pR EcHNVO/DMkcDPcQkZBqIu1ossuM/N0ZQxxUn8ppygzoN3bz7levCFiuItjrJzmMB i6P0EAl0b1g= =ENnh -----END PGP SIGNATURE----- Mon Jun 5 05:29:43 UTC 2023 I: Checking whether the package is not for us Mon Jun 5 05:29:43 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net. Mon Jun 5 05:29:43 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Mon Jun 5 05:31:02 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. 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 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. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) 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. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19907 files and directories currently installed.) 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 ... 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:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps 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 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 debian/rules binary 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 dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild 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 Mon Jun 5 05:31:02 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Mon Jun 5 05:31:02 UTC 2023 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Mon Jun 5 05:33:03 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Mon Jun 5 05:33:03 UTC 2023 I: ctdopts_1.5-2_amd64.changes: Format: 1.8 Date: Thu, 03 Nov 2022 11:41:50 +0100 Source: ctdopts Binary: python3-ctdopts Architecture: all Version: 1.5-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python3-ctdopts - Gives your Python tools a CTD-compatible interface Changes: ctdopts (1.5-2) unstable; urgency=medium . * Team upload. * Enable uscan creating a sensible file name * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: a50b028c136a30c4d237e8370dd45055a0426258 5450 ctdopts_1.5-2_amd64.buildinfo 025e118c9df065ececa92197d653700d448b390c 22424 python3-ctdopts_1.5-2_all.deb Checksums-Sha256: d8009328d07dfaba57718a2797420057d349d9bd7d55c41e0989ec752d2f0fe4 5450 ctdopts_1.5-2_amd64.buildinfo ec1975cc4cdef1ffe3dc004d103d3e1f1fcaa32becd5c6ef364504732385a0a5 22424 python3-ctdopts_1.5-2_all.deb Files: 48a119a33ea7c77d8d992d5d732f4c34 5450 python optional ctdopts_1.5-2_amd64.buildinfo 75a0e7047c348c1e061b0d8f28b920ad 22424 python optional python3-ctdopts_1.5-2_all.deb Mon Jun 5 05:33:04 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.JsXeBiVE/ctdopts_1.5-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.JsXeBiVE/ctdopts_1.5-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.JsXeBiVE/ctdopts_1.5-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.JsXeBiVE/b1/ctdopts_1.5-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.JsXeBiVE/b2/ctdopts_1.5-2_amd64.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: 0.300s) 0.300s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.014s) 0.014s 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 05:33:05 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Mon Jun 5 05:33:05 UTC 2023 I: ctdopts from bookworm built successfully and reproducibly on amd64. Mon Jun 5 05:33:06 UTC 2023 I: Submitting .buildinfo files to external archives: Mon Jun 5 05:33:06 UTC 2023 I: Submitting 8.0K b1/ctdopts_1.5-2_amd64.buildinfo.asc Mon Jun 5 05:33:08 UTC 2023 I: Submitting 8.0K b2/ctdopts_1.5-2_amd64.buildinfo.asc Mon Jun 5 05:33:09 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jun 5 05:33:09 UTC 2023 I: Done submitting .buildinfo files. Mon Jun 5 05:33:09 UTC 2023 I: Removing signed ctdopts_1.5-2_amd64.buildinfo.asc files: removed './b1/ctdopts_1.5-2_amd64.buildinfo.asc' removed './b2/ctdopts_1.5-2_amd64.buildinfo.asc'