Mon Jul 26 09:57:07 UTC 2021 I: starting to build ctdopts/bullseye/arm64 on jenkins on '2021-07-26 09:56' Mon Jul 26 09:57:07 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_16/22117/console.log Mon Jul 26 09:57:07 UTC 2021 I: Downloading source for bullseye/ctdopts=1.4-2 --2021-07-26 09:57:07-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/ctdopts/ctdopts_1.4-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2058 (2.0K) Saving to: ‘ctdopts_1.4-2.dsc’ 0K .. 100% 73.0M=0s 2021-07-26 09:57:07 (73.0 MB/s) - ‘ctdopts_1.4-2.dsc’ saved [2058/2058] Mon Jul 26 09:57:07 UTC 2021 I: ctdopts_1.4-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ctdopts Binary: python3-ctdopts Architecture: all Version: 1.4-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://github.com/WorkflowConversion/CTDopts Standards-Version: 4.5.0 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: 9d12bcc4f9abbb81de89cce3b7ca20e0346d2b02 34883 ctdopts_1.4.orig.tar.gz b99c62422907e82be78a8672601e02f6fbd31bbb 3900 ctdopts_1.4-2.debian.tar.xz Checksums-Sha256: 75c5641ba7bc3b7a4f3693ba03655c77558553a211fe37b61aaf2b5bd9e19ab0 34883 ctdopts_1.4.orig.tar.gz 3ecd345fc10c1d9865479b2660bf598aaca83bafaca7906660f6aaa80d6fbc26 3900 ctdopts_1.4-2.debian.tar.xz Files: 7305d5e688f016a74b414a97d4e5a8b1 34883 ctdopts_1.4.orig.tar.gz cadf1e9a57f840cfd809b3f0ce26c956 3900 ctdopts_1.4-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+gZ4sRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF5VQ//QRdPhJrcxuUjejYjfQXSzFSuZbQFATeA aJq3ElPdVrmdRZy2ny67zz2ERthfpqEJLOF6uugkusSb2O8fyCIzeBcf7UjNvHqq 4m28Odg8WO1jbNAROEIBAKZq9QsY8t6ZNKNC4c+qQSXmV/mBkBG+BHuh6EG47XYp dEr20Y0lzQxRYRfXRSjVqnVaooAM68oFjEid4CFHRok/YkbS1sZswDYhvPmFsmwh 0sqcUuUChRQQ4s42rmuKUQ3zKXsDlWRxSOXSs6oURgwnkJhCK9qq9OtQCHuwkCwu AHSL8F+eZZmgLOXl0owBJDjNvn8/cQeZwgJDPJFrkvc4eDrUEOQ8x0x7B6DZ+E3r plaa9ZWjVBttiu64UU0PVjDy9TLIHNk7171iA+fxNCg87klpIMgiOajO1qs6rsBI aiSeZ14F1yp39LIxiXhnkkCd6XEkxL+pbZaVi5/05DNK3jGl8CqQGLgWa1p/hVtZ ppz1yFehbGIWgN1PkwSuBU3n6/y7g4nV+uSURFvsHqYnhktLwM7/KpX2zlm2HzUd wtD7ECgUF2WWw2GzQek7rvsWEqLLppNYPKuYytIq6UgIVu5QUY2DHLci+nDCR+jh +UrJHdS5SumGoxdU6lgKR5T1H84yZk6FkM8st1lmt34bFljj32kp1+rRIn2CxNcw HPTktT7KuuY= =3QJ5 -----END PGP SIGNATURE----- Mon Jul 26 09:57:07 UTC 2021 I: Checking whether the package is not for us Mon Jul 26 09:57:07 UTC 2021 I: Starting 1st build on remote node codethink12-arm64.debian.net. Mon Jul 26 09:57:07 UTC 2021 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Mon Jul 26 09:57:56 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 25 21:57:09 -12 2021 I: pbuilder-time-stamp: 1627293429 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.hCvL9n89/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 2 08:09:47 2020 -12 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/28083/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='28083' 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/tmp.LXww9qXtPa/pbuilderrc_CFeU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/b1 --logfile b1/build.log ctdopts_1.4-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 24 21:25 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/28083/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: arm64 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 ... 19646 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 24.2 MB of archives. After unpacking 91.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 2to3 all 3.9.2-3 [22.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 python3-tz all 2021.1-1 [34.8 kB] Fetched 24.2 MB in 1s (47.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/ctdopts-1.4/ && 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_1.4-2_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 arm64 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-arm64' 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_arm64.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/28083 and its subdirectories I: Current time: Sun Jul 25 21:57:55 -12 2021 I: pbuilder-time-stamp: 1627293475 Mon Jul 26 09:57:57 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Mon Jul 26 09:57:57 UTC 2021 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Mon Jul 26 09:58:53 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Mon Jul 26 09:58:54 UTC 2021 I: ctdopts_1.4-2_arm64.changes: Format: 1.8 Date: Mon, 02 Nov 2020 21:06:31 +0100 Source: ctdopts Binary: python3-ctdopts Architecture: all Version: 1.4-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: python3-ctdopts - Gives your Python tools a CTD-compatible interface Closes: 972528 Changes: ctdopts (1.4-2) unstable; urgency=medium . * Team upload. * do not use getchildren (thanks for the patch to Michael Hudson-Doyle) Closes: #972528 Checksums-Sha1: dd2e8c33b3d4498cabb19c8159a025ff32a4c1d0 5205 ctdopts_1.4-2_arm64.buildinfo b10cd35f693e6f512be6469cd94d04984688e9f5 22500 python3-ctdopts_1.4-2_all.deb Checksums-Sha256: e5d244fb2690fe579ffe561bd4afe018b48b00d1753c99f5c3724be4034b3c8d 5205 ctdopts_1.4-2_arm64.buildinfo 095cb23a2f7b48f4f5bd8d3c673a626886590107d901e1d6320dda7109278471 22500 python3-ctdopts_1.4-2_all.deb Files: 784ec2ab12488c51f7a1d5460be20cf9 5205 python optional ctdopts_1.4-2_arm64.buildinfo d89d803d53a3be2d60b0ed7dbc57eb38 22500 python optional python3-ctdopts_1.4-2_all.deb Mon Jul 26 09:58:55 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/ctdopts_1.4-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/ctdopts_1.4-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/ctdopts_1.4-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/b1/ctdopts_1.4-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.LXww9qXtPa/b2/ctdopts_1.4-2_arm64.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: 0.286s) 0.286s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Jul 26 09:58:57 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Jul 26 09:58:57 UTC 2021 I: ctdopts from bullseye built successfully and reproducibly on arm64. Mon Jul 26 09:58:58 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Jul 26 09:58:58 UTC 2021 I: Submitting 8.0K b1/ctdopts_1.4-2_arm64.buildinfo.asc Mon Jul 26 09:58:59 UTC 2021 I: Submitting 8.0K b2/ctdopts_1.4-2_arm64.buildinfo.asc Mon Jul 26 09:59:01 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jul 26 09:59:01 UTC 2021 I: Done submitting .buildinfo files. Mon Jul 26 09:59:01 UTC 2021 I: Removing signed ctdopts_1.4-2_arm64.buildinfo.asc files: removed './b1/ctdopts_1.4-2_arm64.buildinfo.asc' removed './b2/ctdopts_1.4-2_arm64.buildinfo.asc'