I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 27 08:17:15 +14 2021 I: pbuilder-time-stamp: 1635272235 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_1.4-2.dsc] I: copying [./ctdopts_1.4.orig.tar.gz] I: copying [./ctdopts_1.4-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.CCC_nEZZ/trustedkeys.kbx': General error gpgv: Signature made Tue Nov 3 10:09:47 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ctdopts_1.4-2.dsc dpkg-source: info: extracting ctdopts in ctdopts-1.4 dpkg-source: info: unpacking ctdopts_1.4.orig.tar.gz dpkg-source: info: unpacking ctdopts_1.4-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3 dpkg-source: info: applying bc082bd2e20c81fdf33cf96f8241f6cce68f2f8d.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2914733/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2914733/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2914733/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3b0665aaf01a427c887ba903687b8772 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2914733 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DRm5BoN4nL/pbuilderrc_BcE7 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DRm5BoN4nL/b2 --logfile b2/build.log ctdopts_1.4-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Oct 27 08:17 sh -> bash lrwxrwxrwx 1 root root 4 Oct 22 01:41 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/2914733/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 ... 19655 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} libicu67{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{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} python3.9{a} python3.9-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, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 24.7 MB of archives. After unpacking 92.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 2to3 all 3.9.2-3 [22.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 python3-distutils all 3.9.2-1 [143 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 python3-setuptools all 52.0.0-4 [366 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Fetched 24.7 MB in 0s (59.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known I: Running cd /build/ctdopts-1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ctdopts_1.4-2_source.changes dpkg-buildpackage: info: source package ctdopts dpkg-buildpackage: info: source version 1.4-2 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:232: python3.9 setup.py clean running clean removing '/build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' 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:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/ctdopts-1.4' dh_auto_build I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts copying CTDopts/CTDopts.py -> /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts copying CTDopts/__init__.py -> /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts /usr/lib/python3/dist-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process. warnings.warn( Fixing /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/CTDopts.py /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/CTDopts.py /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma # 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 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-1.4' debian/rules override_dh_auto_test make[1]: Entering directory '/build/ctdopts-1.4' export PYBUILD_SYSTEM=custom; dh_auto_test I: pybuild base:232: PYTHONPATH=/build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build python3.9 debian/example.py /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/CTDopts.py:1070: UserWarning: Argument restrictions for positive_int violated. Restriction: 0:. Value: -5 warnings.warn('Argument restrictions for %s violated. Restriction: %s. Value: %s' % /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/CTDopts.py:1070: 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-1.4' 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:232: /usr/bin/python3 setup.py install --root /build/ctdopts-1.4/debian/python3-ctdopts running install running build running build_py running install_lib creating /build/ctdopts-1.4/debian/python3-ctdopts/usr creating /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib creating /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9 creating /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages creating /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts creating /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts/__pycache__ copying /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/__pycache__/CTDopts.cpython-39.pyc -> /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts/__pycache__ copying /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/__pycache__/__init__.cpython-39.pyc -> /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts/__pycache__ copying /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/__init__.py -> /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts copying /build/ctdopts-1.4/.pybuild/cpython3_3.9_CTDopts/build/CTDopts/CTDopts.py -> /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts byte-compiling /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts/CTDopts.py to CTDopts.cpython-39.pyc running install_egg_info running egg_info creating CTDopts.egg-info writing CTDopts.egg-info/PKG-INFO writing dependency_links to CTDopts.egg-info/dependency_links.txt writing requirements to CTDopts.egg-info/requires.txt writing top-level names to CTDopts.egg-info/top_level.txt writing manifest file 'CTDopts.egg-info/SOURCES.txt' reading manifest file 'CTDopts.egg-info/SOURCES.txt' writing manifest file 'CTDopts.egg-info/SOURCES.txt' Copying CTDopts.egg-info to /build/ctdopts-1.4/debian/python3-ctdopts/usr/lib/python3.9/dist-packages/CTDopts-1.4.egg-info Skipping SOURCES.txt running install_scripts 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_1.4-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ctdopts_1.4-2_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: user script /srv/workspace/pbuilder/2914733/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2914733/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2914733 and its subdirectories I: Current time: Wed Oct 27 08:18:02 +14 2021 I: pbuilder-time-stamp: 1635272282