Diff of the two buildlogs: -- --- b1/build.log 2023-04-29 14:19:20.844111945 +0000 +++ b2/build.log 2023-04-29 14:28:16.820579774 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 31 08:32:08 -12 2024 -I: pbuilder-time-stamp: 1717187528 +I: Current time: Sun Apr 30 04:19:25 +14 2023 +I: pbuilder-time-stamp: 1682777965 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./cwltool_3.0.20210124104916-3+deb11u1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.pYLzyfR9/trustedkeys.kbx': General error -gpgv: Signature made Fri Dec 2 06:19:48 2022 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.9iAwMEC_/trustedkeys.kbx': General error +gpgv: Signature made Sat Dec 3 08:19:48 2022 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cwltool_3.0.20210124104916-3+deb11u1.dsc @@ -33,135 +33,166 @@ dpkg-source: info: applying add_interps I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23481/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1815/tmp/hooks/D01_modify_environment starting +debug: Running on codethink16-arm64. +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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 30 04:19 /bin/sh -> /bin/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/1815/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1815/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' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='bullseye' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + 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='23481' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=1815 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.0KuKjts6/pbuilderrc_EVaQ --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0KuKjts6/b1 --logfile b1/build.log cwltool_3.0.20210124104916-3+deb11u1.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' + 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/r-b-build.0KuKjts6/pbuilderrc_9zre --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0KuKjts6/b2 --logfile b2/build.log cwltool_3.0.20210124104916-3+deb11u1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink9-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Mar 27 2022 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 Jan 20 2022 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 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 64856 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 182496 Jan 24 2023 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 93744 Apr 9 2022 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 157864 Jan 20 2022 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 Jan 20 2022 more - -rwsr-xr-x 1 root root 51360 Jan 20 2022 mount - -rwxr-xr-x 1 root root 14496 Jan 20 2022 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 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 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 May 23 03:55 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 Jan 20 2022 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 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 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jan 20 2022 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 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 5898 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 8049 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/23481/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Mar 28 2022 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jan 21 2022 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 22:23 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 22:23 fgrep + -rwxr-xr-x 1 root root 64856 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 182496 Jan 25 22:23 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 93744 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 157864 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jan 21 2022 more + -rwsr-xr-x 1 root root 51360 Jan 21 2022 mount + -rwxr-xr-x 1 root root 14496 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Apr 30 04:19 sh -> /bin/bash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jan 21 2022 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jan 21 2022 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1815/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -422,7 +453,7 @@ Get: 169 http://deb.debian.org/debian bullseye/main arm64 python3-schema-salad all 7.0.20210124093443-1 [302 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 python3-shellescape all 3.4.1-4 [4884 B] Get: 171 http://deb.debian.org/debian bullseye/main arm64 python3-sparqlwrapper all 1.8.5-1 [35.2 kB] -Fetched 52.9 MB in 12s (4484 kB/s) +Fetched 52.9 MB in 3s (17.8 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 ... 19698 files and directories currently installed.) @@ -1137,7 +1168,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/cwltool-3.0.20210124104916/ && 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 > ../cwltool_3.0.20210124104916-3+deb11u1_source.changes +I: user script /srv/workspace/pbuilder/1815/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1815/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/cwltool-3.0.20210124104916/ && 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 > ../cwltool_3.0.20210124104916-3+deb11u1_source.changes dpkg-buildpackage: info: source package cwltool dpkg-buildpackage: info: source version 3.0.20210124104916-3+deb11u1 dpkg-buildpackage: info: source distribution bullseye @@ -2652,7 +2687,7 @@ cd {build_dir}; export PYTHONPATH=$(pwd); {interpreter} -m pytest \ -k 'not test_http_path_mapping and not test_pack and not test_get_subgraph and not test_use_metadata and not test_load_graph_fragment_from_packed and not test_udocker_usage_should_not_write_cid_file and not test_udocker_should_display_memory_usage' \ -n auto --dist=loadfile --ignore cwltool/schemas/ -s --pyargs cwltool" dh_auto_test -I: pybuild base:232: cd /build/cwltool-3.0.20210124104916; export PATH=/build/cwltool-3.0.20210124104916/debian/python3-cwltool/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games ; cd /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build; export PYTHONPATH=/build/cwltool-3.0.20210124104916; python3.9 -m pytest -k 'not test_http_path_mapping and not test_pack and not test_get_subgraph and not test_use_metadata and not test_load_graph_fragment_from_packed and not test_udocker_usage_should_not_write_cid_file and not test_udocker_should_display_memory_usage' -n auto --dist=loadfile --ignore cwltool/schemas/ -s --pyargs cwltool +I: pybuild base:232: cd /build/cwltool-3.0.20210124104916; export PATH=/build/cwltool-3.0.20210124104916/debian/python3-cwltool/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path ; cd /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build; export PYTHONPATH=/build/cwltool-3.0.20210124104916; python3.9 -m pytest -k 'not test_http_path_mapping and not test_pack and not test_get_subgraph and not test_use_metadata and not test_load_graph_fragment_from_packed and not test_udocker_usage_should_not_write_cid_file and not test_udocker_should_display_memory_usage' -n auto --dist=loadfile --ignore cwltool/schemas/ -s --pyargs cwltool ============================= test session starts ============================== platform linux -- Python 3.9.2, pytest-6.0.2, py-1.10.0, pluggy-0.13.0 rootdir: /build/cwltool-3.0.20210124104916, configfile: setup.cfg @@ -2660,21 +2695,21 @@ gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I gw0 [418] / gw1 [418] / gw2 [418] / gw3 [418] / gw4 [418] / gw5 [418] / gw6 [418] / gw7 [418] -ssssssResolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' -ssssResolved '/build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' -sResolved '/build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' -Resolved 'foo.cwl' to 'baz:bar/foo.cwl' -ssURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? -sssssssssssINFO 3.0.20210124104916 +sssssResolved 'foo.cwl' to 'baz:bar/foo.cwl' +Resolved '/build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' +sssssURI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? +Resolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' +ssResolved '/build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' +ssssssssssssINFO 3.0.20210124104916 INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/missing_cwlVersion.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/missing_cwlVersion.cwl' INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/missing_cwlVersion.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/missing_cwlVersion.cwl' ERROR Tool definition failed validation: No cwlVersion found. Use the following syntax in your CWL document to declare the version: cwlVersion: . Note: if this is a CWL draft-2 (pre v1.0) document then it will need to be upgraded first. .INFO 3.0.20210124104916 -INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/wrong_cwlVersion.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/wrong_cwlVersion.cwl' +INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' ERROR Tool definition failed validation: The CWL reference runner no longer supports pre CWL v1.0 documents. Supported versions are: @@ -2689,71 +2724,68 @@ v1.2.0-dev5 (with --enable-dev flag only) .INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/no-parameters-echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/no-parameters-echo.cwl' -../../../tests/wf/default_path.cwl:9:7: Warning: Field `path` contains undefined reference to - `file:///build/cwltool-3.0.20210124104916/tests/wf/default.txt` -........URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? +URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section? URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section? -....[job echo.cwl] /tmp/191ro7jw$ echo \ - foo > /tmp/191ro7jw/out.txt -...[job echo.cwl] completed success -....s....................INFO 3.0.20210124104916 -.INFO Resolved 'foo.cwl' to 'baz:bar/foo.cwl' -..URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? -....................[job iwdr-entry.cwl] /tmp/nxzu_c_5$ cat \ - example.conf -..CONFIGVAR=hello -.[job iwdr-entry.cwl] completed success -..ssERROR Workflow or tool uses unsupported feature: -Docker is required to run this tool: docker executable is not available -s.sssssssResolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' -.sssss.sss.sss.Resolved '/build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' -INFO [job no-parameters-echo.cwl] /tmp/t41gljgt$ echo > /tmp/t41gljgt/35f1dfe96668455c7eca33db5806493ab218311b ../../../tests/wf/default_path.cwl:9:7: Warning: Field `path` contains undefined reference to `file:///build/cwltool-3.0.20210124104916/tests/wf/default.txt` -INFO [job no-parameters-echo.cwl] completed success +...............[job echo.cwl] /tmp/3vzk0ptw$ echo \ + foo > /tmp/3vzk0ptw/out.txt +......[job echo.cwl] completed success +.....s..ss..s.s.s.INFO 3.0.20210124104916 +.s.ss.INFO Resolved 'foo.cwl' to 'baz:bar/foo.cwl' +URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? +.ss.ss..s..Resolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' +.....................INFO [job no-parameters-echo.cwl] /tmp/tvlwcs5r$ echo > /tmp/tvlwcs5r/35f1dfe96668455c7eca33db5806493ab218311b +.ERROR Workflow or tool uses unsupported feature: +Docker is required to run this tool: docker executable is not available +..INFO [job no-parameters-echo.cwl] completed success INFO Final process status is success -..sResolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' -ss....sssResolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' -ssINFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' +..s.Resolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' +s[job iwdr-entry.cwl] /tmp/uw58_it9$ cat \ + example.conf +...CONFIGVAR=hello +[job iwdr-entry.cwl] completed success +.sssINFO 3.0.20210124104916 +sINFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' +sResolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' +sResolved '/build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/default_path.cwl' +../../../tests/wf/default_path.cwl:9:7: Warning: Field `path` contains undefined reference to + `file:///build/cwltool-3.0.20210124104916/tests/wf/default.txt` .Resolved '/build/cwltool-3.0.20210124104916/tests/wf/1st-workflow.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/1st-workflow.cwl' -INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' -INFO [job timelimit.cwl] /tmp/essrzafg$ sleep \ - 3 +.sssssINFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/iwdr-entry.cwl' Resolved '/build/cwltool-3.0.20210124104916/tests/wf/1st-workflow.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/1st-workflow.cwl' -...........INFO [job timelimit.cwl] Max memory used: 0MiB -.INFO [job timelimit.cwl] completed success -INFO Final process status is success -.INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' -...........................[workflow ] starting step step1 +INFO [job timelimit.cwl] /tmp/xxxfpnox$ sleep \ + 3 +...................INFO [job timelimit.cwl] Max memory used: 0MiB +INFO [job timelimit.cwl] completed success +.INFO Final process status is success +...INFO 3.0.20210124104916 +.INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/timelimit.cwl' +.................[workflow ] starting step step1 +[workflow ] start [step step1] start -.[workflow ] start -[job step1] /tmp/gne83oaj$ wc \ - -l < /tmp/ngkjk3ps/stg6eea8ee0-8030-4990-9311-d814efaf5e5e/whale.txt > /tmp/gne83oaj/output -.[job step1] completed success -.[step step1] completed success +[job step1] /tmp/z6o1js6a$ wc \ + -l < /tmp/6e55expa/stg298602b6-a7e2-4f58-939d-6d9c7144b2b8/whale.txt > /tmp/z6o1js6a/output +..[job step1] completed success +[step step1] completed success [workflow ] starting step step2 [step step2] start ...............................................Resolved '/build/cwltool-3.0.20210124104916/tests/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo.cwl' -[job echo.cwl] /tmp/leyxnrph$ echo \ - foo > /tmp/leyxnrph/out.txt +[job echo.cwl] /tmp/gm6621js$ echo \ + foo > /tmp/gm6621js/out.txt [job echo.cwl] completed success .Resolved '/build/cwltool-3.0.20210124104916/tests/echo_broken_outputs.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/echo_broken_outputs.cwl' ...Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatterfail.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatterfail.cwl' -[step step2] completed success -[workflow ] completed success -.[workflow ] start +[workflow ] start [workflow ] starting step step1 [step step1] start -Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' [workflow step1] start [workflow step1] starting step sstep1 [step sstep1] start -[job sstep1] /tmp/a3xtoqwt$ python3 \ +[job sstep1] /tmp/olib2ht2$ python3 \ -c \ 'import sys print(sys.argv[1]) @@ -2767,13 +2799,16 @@ exit(1) ' \ 1 +[step step2] completed success +[workflow ] completed success +.Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' 1 [job sstep1] completed success [step sstep1] completed success [workflow step1] starting step sstep2 [step sstep2] start -[job sstep2] /tmp/cg5tire_$ cat \ - /tmp/qc4kraer/stg807b37c7-200c-4c9b-bfe2-d56e233f62c1/foo1.txt +[job sstep2] /tmp/_6vhueea$ cat \ + /tmp/i0vw56ik/stg26057d16-79fa-430c-8ae1-195ad601bf0a/foo1.txt 1 [job sstep2] completed success [step sstep2] completed success @@ -2782,7 +2817,7 @@ [workflow step1_2] start [workflow step1_2] starting step sstep1_2 [step sstep1_2] start -[job sstep1_2] /tmp/e4vcavks$ python3 \ +[job sstep1_2] /tmp/aw0kepw8$ python3 \ -c \ 'import sys print(sys.argv[1]) @@ -2807,7 +2842,7 @@ [workflow step1_3] start [workflow step1_3] starting step sstep1_3 [step sstep1_3] start -[job sstep1_3] /tmp/qujomwlh$ python3 \ +[job sstep1_3] /tmp/qv9d6gk3$ python3 \ -c \ 'import sys print(sys.argv[1]) @@ -2826,8 +2861,8 @@ [step sstep1_3] completed success [workflow step1_3] starting step sstep2_3 [step sstep2_3] start -[job sstep2_2] /tmp/aaxsfvcm$ cat \ - /tmp/ulmqzdny/stgdc3ed18d-25b3-4ceb-97aa-3625670aae3a/foo3.txt +[job sstep2_2] /tmp/3jn6gz0v$ cat \ + /tmp/0f6yoo5l/stgf393c544-f499-47e8-accc-f0b4469bc676/foo3.txt 3 [job sstep2_2] completed success [step sstep2_3] completed success @@ -2839,21 +2874,9 @@ URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section? URI prefix 'baz' of 'baz:bar/foo.cwl' not recognized, are you missing a $namespaces section? URI prefix 'baz' of 'baz:bar/foo.cwl#bar/foo.cwl' not recognized, are you missing a $namespaces section? -.....[job _:438c1723-06cc-4ac1-88b2-65cb7ff0def9] initializing from _:438c1723-06cc-4ac1-88b2-65cb7ff0def9 -[job _:438c1723-06cc-4ac1-88b2-65cb7ff0def9] {} -[job _:438c1723-06cc-4ac1-88b2-65cb7ff0def9] path mappings is {} -[job _:438c1723-06cc-4ac1-88b2-65cb7ff0def9] command line bindings is [] -.[job _:37669511-9a39-499c-89d9-0a842cec8c01] initializing from _:37669511-9a39-499c-89d9-0a842cec8c01 -[job _:37669511-9a39-499c-89d9-0a842cec8c01] {} -[job _:37669511-9a39-499c-89d9-0a842cec8c01] path mappings is {} -[job _:37669511-9a39-499c-89d9-0a842cec8c01] command line bindings is [] -.s...ssssINFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' -ERROR Workflow or tool uses unsupported feature: -Singularity is required to run this tool: singularity executable is not available -.sssINFO 3.0.20210124104916 -INFO Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl' -.ERROR Tool definition failed validation: +.....INFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' +ERROR Tool definition failed validation: ../../../tests/wf/generator/pytoolgen.cwl:10:1: checking field `requirements` ../../../tests/wf/generator/pytoolgen.cwl:22:5: checking item Field `class` contains undefined reference to @@ -2861,13 +2884,17 @@ ../../../tests/wf/generator/pytoolgen.cwl:5:1: Field `class` contains undefined reference to `file:///build/cwltool-3.0.20210124104916/tests/wf/generator/ProcessGenerator` ../../../tests/wf/generator/pytoolgen.cwl:10:1: checking object - `../../../tests/wf/generator/pytoolgen.cwl#2ed19189-107e-4ab6-8510-0e0fedba1fb2` + `../../../tests/wf/generator/pytoolgen.cwl#d3be5f65-6d99-40cf-bd97-63a6ed52ddef` ../../../tests/wf/generator/pytoolgen.cwl:20:3: checking field `requirements` ../../../tests/wf/generator/pytoolgen.cwl:22:5: checking item Field `class` contains undefined reference to `http://commonwl.org/cwltool#LoadListingRequirement` INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' +ERROR Workflow or tool uses unsupported feature: +Singularity is required to run this tool: singularity executable is not available +.sss..s....ssssINFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' ERROR Tool definition failed validation: ../../../tests/wf/timelimit.cwl:12:1: checking field `requirements` ../../../tests/wf/timelimit.cwl:13:3: checking item @@ -2875,61 +2902,30 @@ `http://commonwl.org/cwltool#TimeLimit` INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/timelimit-fail.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/timelimit-fail.cwl' -.INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' +.....sssINFO 3.0.20210124104916 +INFO Resolved 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4' to 'https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-md5sum/versions/1.0.4/plain-CWL/descriptor/Dockstore.cwl' [workflow _2] starting step step1_2 [step step1_2] start [step step1_2] start [workflow _2] start -[job step1_2] /tmp/9brw_sai$ echo \ +[job step1_2] /tmp/unzrknjt$ echo \ -n \ foo \ one \ - three > /tmp/9brw_sai/step1_out -[job step1_3] /tmp/c_bk6_mh$ echo \ + three > /tmp/unzrknjt/step1_out +[job step1_3] /tmp/bgg6uk1j$ echo \ -n \ foo \ two \ - four > /tmp/c_bk6_mh/step1_out + four > /tmp/bgg6uk1j/step1_out [job step1_2] completed success [job step1_3] completed success [step step1_2] completed success [workflow _2] completed success -...........DEBUG Parsed job order from command line: { - "id": "/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script", - "input": { - "class": "File", - "location": "file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script" - } -} -INFO Final process status is success -INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' -.INFO 3.0.20210124104916 -INFO Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl' -[workflow _2] start -[workflow _2] starting step step3 -[step step3] start -[job step3] /tmp/ogam0vz_$ python3 \ - -c \ - 'import sys -print(sys.argv[1]) -if sys.argv[1] == "2": - exit(1) -else: - f = open("foo"+sys.argv[1]+".txt", "wb") - content = sys.argv[1]+"\n" - f.write(content.encode('"'"'utf-8'"'"')) -if sys.argv[1] == "5": - exit(1) -' \ - 5 -5 -[job step3] completed permanentFail -[step step3] completed permanentFail +...........[workflow _2] start [workflow _2] starting step step1_2 [step step1_2] start -[job step1] /tmp/olrv7r7x$ python3 \ +[job step1] /tmp/tt7ayenk$ python3 \ -c \ 'import sys print(sys.argv[1]) @@ -2948,7 +2944,7 @@ [step step1_2] completed success [workflow _2] starting step step2 [step step2] start -[job step2] /tmp/xp7o5kqt$ python3 \ +[job step2] /tmp/ysea51ny$ python3 \ -c \ 'import sys print(sys.argv[1]) @@ -2968,91 +2964,122 @@ [job step2] completed permanentFail [step step2] Output is missing expected field file:///build/cwltool-3.0.20210124104916/tests/wf/wffail.cwl#step2/out [step step2] completed permanentFail +[workflow _2] starting step step3 +[step step3] start +[job step3] /tmp/fhohfpk4$ python3 \ + -c \ + 'import sys +print(sys.argv[1]) +if sys.argv[1] == "2": + exit(1) +else: + f = open("foo"+sys.argv[1]+".txt", "wb") + content = sys.argv[1]+"\n" + f.write(content.encode('"'"'utf-8'"'"')) +if sys.argv[1] == "5": + exit(1) +' \ + 5 +5 +[job step3] completed permanentFail +[step step3] completed permanentFail [workflow _2] completed permanentFail -..INFO 3.0.20210124104916 +..DEBUG Parsed job order from command line: { + "id": "/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script", + "input": { + "class": "File", + "location": "file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script" + } +} +INFO Final process status is success +INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/trick_defaults.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/trick_defaults.cwl' -.INFO 3.0.20210124104916 +INFO 3.0.20210124104916 +.INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' +INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' -INFO [job timelimit-fail.cwl] /tmp/37_vnmvb$ sleep \ +INFO [job 040af793-223e-4b3f-bdcf-89d1cb20ea03] /tmp/kh76ix1t$ python3 \ + inp.py > /tmp/kh76ix1t/main.cwl +INFO [job 040af793-223e-4b3f-bdcf-89d1cb20ea03] completed success +INFO [job main.cwl] /tmp/50cqq1i7$ echo \ + zipper +zipper +INFO [job main.cwl] completed success +INFO Final process status is success +INFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' +INFO [job timelimit-fail.cwl] /tmp/44hmk8nz$ sleep \ 5 -.WARNING [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated +..INFO 3.0.20210124104916 +INFO Resolved '#workflow/github.com/dockstore-testing/md5sum-checker:develop' to 'https://dockstore.org/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fdockstore-testing%2Fmd5sum-checker/versions/develop/plain-CWL/descriptor/md5sum-workflow.cwl' +WARNING [job timelimit-fail.cwl] exceeded time limit of 3 seconds and will be terminated INFO [job timelimit-fail.cwl] Max memory used: 0MiB WARNING [job timelimit-fail.cwl] completed permanentFail WARNING Final process status is permanentFail -.INFO [job 619055fe-f7ca-4a96-8210-71c9f6d2676a] /tmp/6hu9qs8h$ python3 \ - inp.py > /tmp/6hu9qs8h/main.cwl -INFO [job 619055fe-f7ca-4a96-8210-71c9f6d2676a] completed success -INFO [job main.cwl] /tmp/osn0aibp$ echo \ - zipper -INFO [workflow ] start +.INFO [workflow ] start INFO [workflow ] starting step step1 INFO [step step1] start -zipper -INFO [job step1] /tmp/vachvpkw$ echo \ +INFO [job step1] /tmp/g55bk64q$ echo \ -n \ foo \ INP1 \ - INP2 > /tmp/vachvpkw/step1_out -INFO [job main.cwl] completed success -INFO Final process status is success + INP2 > /tmp/g55bk64q/step1_out INFO [job step1] completed success INFO [step step1] completed success INFO [workflow ] completed success INFO Final process status is success .INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/generator/zing.cwl' -INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl' -usage: /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script +usage: /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script [-h] --input INPUT [job_order] -/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script: error: the following arguments are required: --input +/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script: error: the following arguments are required: --input INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script' -......../tmp/l2u3x7mp/stg1fd408a6-e212-45be-961a-94644449499a/tmp4/alpha/foxtrot -......Resolved '/build/cwltool-3.0.20210124104916/tests/wf/vf-concat.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/vf-concat.cwl' -.INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' -ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information. -The error was: 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl#main/dummy_target' -.INFO 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.json' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.json' -.INFO [job 27a6b1a4-6824-4f21-9ed8-a7f087fed8df] /tmp/kjoxjib8$ python3 \ - inp.py > /tmp/kjoxjib8/main.cwl -INFO [job 27a6b1a4-6824-4f21-9ed8-a7f087fed8df] completed success -INFO [job main.cwl_2] /tmp/wuxw6cxt$ echo \ +INFO Resolved '/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' to 'file:///build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script' +INFO [job 003cd499-8e34-4b65-acd2-93b61377ae75] /tmp/o9_ptvng$ python3 \ + inp.py > /tmp/o9_ptvng/main.cwl +INFO [job 003cd499-8e34-4b65-acd2-93b61377ae75] completed success +INFO [job main.cwl_2] /tmp/vo1zober$ echo \ zipper zipper INFO [job main.cwl_2] completed success INFO Final process status is success .INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/hello_single_tool.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/hello_single_tool.cwl' +.INFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' +../tmp/1iwpv_yh/stgb5607d4b-90cb-4c3c-8e06-9b7d272874c6/tmp4/alpha/foxtrot +......Resolved '/build/cwltool-3.0.20210124104916/tests/wf/vf-concat.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/vf-concat.cwl' +.......ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information. +The error was: 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.cwl#main/dummy_target' +.INFO 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.json' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/scatter-wf4.json' DEBUG Parsed job order from command line: { - "id": "/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw1/test_dont_require_inputs0/script", + "id": "/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/popen-gw5/test_dont_require_inputs0/script", "input": null } INFO Final process status is success .Resolved '/build/cwltool-3.0.20210124104916/tests/with_doc.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/with_doc.cwl' .Resolved '/build/cwltool-3.0.20210124104916/tests/without_doc.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/without_doc.cwl' -.[job vf-concat.cwl] /tmp/h8ad82t6$ echo \ - 'a string' > /tmp/h8ad82t6/output.txt +.[job vf-concat.cwl] /tmp/iya2cyi6$ echo \ + 'a string' > /tmp/iya2cyi6/output.txt [job vf-concat.cwl] completed success -...INFO 3.0.20210124104916 +....INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/count-lines1-wf.cwl' -INFO [workflow _2] start +INFO /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__main__.py 3.0.20210124104916 +INFO Resolved '/build/cwltool-3.0.20210124104916/tests/utf_doc_example.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/utf_doc_example.cwl' +..INFO [workflow _2] start INFO [workflow _2] starting step step1_2 INFO [step step1_2] start -INFO [job step1_2] /tmp/lf1kl5d9$ echo \ +INFO [job step1_2] /tmp/un4yhbif$ echo \ -n \ foo \ INP1 \ - INP2 > /tmp/lf1kl5d9/step1_out + INP2 > /tmp/un4yhbif/step1_out INFO [job step1_2] completed success INFO [step step1_2] completed success INFO [workflow _2] completed success INFO Final process status is success -....INFO /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__main__.py 3.0.20210124104916 -INFO Resolved '/build/cwltool-3.0.20210124104916/tests/utf_doc_example.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/utf_doc_example.cwl' -..................................Resolved '/build/cwltool-3.0.20210124104916/tests/test_bad_outputs_wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/test_bad_outputs_wf.cwl' +...................................Resolved '/build/cwltool-3.0.20210124104916/tests/test_bad_outputs_wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/test_bad_outputs_wf.cwl' Validation failed at Traceback (most recent call last): File "/build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/workflow.py", line 105, in __init__ @@ -3098,17 +3125,17 @@ } ] .Resolved '/build/cwltool-3.0.20210124104916/tests/checker_wf/broken-wf.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/checker_wf/broken-wf.cwl' -Workflow checker warning: +.Workflow checker warning: +../../../tests/checker_wf/broken-wf.cwl:10:5: Source 'letters0' of type ["string", "int"] may be + incompatible +../../../tests/checker_wf/broken-wf.cwl:42:7: with sink 'echo_in' of type ["string", {"type": + "array", "items": "string"}] ../../../tests/checker_wf/broken-wf.cwl:16:5: Source 'letters2' of type ["string", "int"] may be incompatible ../../../tests/checker_wf/broken-wf.cwl:48:7: with sink 'echo_in' of type {"type": "array", "items": ["string", {"type": "array", "items": "string"}]} source has linkMerge method merge_nested -../../../tests/checker_wf/broken-wf.cwl:10:5: Source 'letters0' of type ["string", "int"] may be - incompatible -../../../tests/checker_wf/broken-wf.cwl:42:7: with sink 'echo_in' of type ["string", {"type": - "array", "items": "string"}] Resolved '/build/cwltool-3.0.20210124104916/tests/checker_wf/broken-wf2.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/checker_wf/broken-wf2.cwl' MPIRequirement with containers is a beta feature .MPIRequirement with containers is a beta feature @@ -3159,8 +3186,8 @@ raise ValidationException("\n".join(validation_errors)) schema_salad.exceptions.ValidationException: ../../../tests/checker_wf/broken-wf3.cwl:38:8: Workflow step output 'All' does not correspond to ../../../tests/checker_wf/functional-wf.cwl:28:1: tool output (expected 'all') -Resolved '/build/cwltool-3.0.20210124104916/tests/non_portable.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/non_portable.cwl' -.../../../tests/non_portable.cwl:18:4: +.Resolved '/build/cwltool-3.0.20210124104916/tests/non_portable.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/non_portable.cwl' +../../../tests/non_portable.cwl:18:4: ../../../tests/non_portable.cwl:18:4: Non-portable reference to /var/spool/cwl detected: '/var/spool/cwl/hi.txt'. ../../../tests/non_portable.cwl:18:4: To fix, replace /var/spool/cwl with $(runtime.outdir) or add ../../../tests/non_portable.cwl:18:4: DockerRequirement to the 'requirements' section and declare @@ -3173,7 +3200,7 @@ ../../../tests/non_portable2.cwl:19:4: DockerRequirement to the 'requirements' section and declare ../../../tests/non_portable2.cwl:19:4: 'dockerOutputDirectory: /var/spool/cwl'. .Resolved '/build/cwltool-3.0.20210124104916/tests/portable.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/portable.cwl' -..INFO 3.0.20210124104916 +.INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/revsort.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/revsort.cwl' INFO 3.0.20210124104916 INFO Resolved '/build/cwltool-3.0.20210124104916/tests/wf/echo.cwl' to 'file:///build/cwltool-3.0.20210124104916/tests/wf/echo.cwl' @@ -3213,7 +3240,7 @@ [step generate_list] completed success [workflow _3] starting step generate_files [step generate_files] start -[job generate_files] initializing from _:3e6f7e3a-1838-4f04-bc21-38728119d7da as part of step generate_files +[job generate_files] initializing from _:2e857dee-c746-461b-9e39-d9fac5847560 as part of step generate_files [job generate_files] { "number": 0 } @@ -3235,13 +3262,13 @@ } ] [job generate_files] initial work dir {} -[job generate_files] /tmp/67d97vww$ echo \ - 0 > /tmp/67d97vww/output.txt +[job generate_files] /tmp/k440iyvk$ echo \ + 0 > /tmp/k440iyvk/output.txt Could not collect memory usage, job ended before monitoring began. [job generate_files] completed success [job generate_files] outputs { "output": { - "location": "file:///tmp/67d97vww/output.txt", + "location": "file:///tmp/k440iyvk/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3251,10 +3278,10 @@ "http://commonwl.org/cwltool#generation": 0 } } -[job generate_files] Removing input staging directory /tmp/m0uhari9 -[job generate_files] Removing temporary directory /tmp/_okaz55t +[job generate_files] Removing input staging directory /tmp/n7vvhuwx +[job generate_files] Removing temporary directory /tmp/3yc_93hc [step generate_files] start -[job generate_files_2] initializing from _:3e6f7e3a-1838-4f04-bc21-38728119d7da as part of step generate_files +[job generate_files_2] initializing from _:2e857dee-c746-461b-9e39-d9fac5847560 as part of step generate_files [job generate_files_2] { "number": 1 } @@ -3276,13 +3303,13 @@ } ] [job generate_files_2] initial work dir {} -[job generate_files_2] /tmp/ekpmrm8z$ echo \ - 1 > /tmp/ekpmrm8z/output.txt +[job generate_files_2] /tmp/jcuddu1e$ echo \ + 1 > /tmp/jcuddu1e/output.txt Could not collect memory usage, job ended before monitoring began. [job generate_files_2] completed success [job generate_files_2] outputs { "output": { - "location": "file:///tmp/ekpmrm8z/output.txt", + "location": "file:///tmp/jcuddu1e/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3292,10 +3319,10 @@ "http://commonwl.org/cwltool#generation": 0 } } -[job generate_files_2] Removing input staging directory /tmp/qv6a0lj8 -[job generate_files_2] Removing temporary directory /tmp/x9rhs0ol +[job generate_files_2] Removing input staging directory /tmp/u6jlzd6i +[job generate_files_2] Removing temporary directory /tmp/hk48rrk_ [step generate_files] start -[job generate_files_3] initializing from _:3e6f7e3a-1838-4f04-bc21-38728119d7da as part of step generate_files +[job generate_files_3] initializing from _:2e857dee-c746-461b-9e39-d9fac5847560 as part of step generate_files [job generate_files_3] { "number": 2 } @@ -3317,13 +3344,13 @@ } ] [job generate_files_3] initial work dir {} -[job generate_files_3] /tmp/f1bl28mw$ echo \ - 2 > /tmp/f1bl28mw/output.txt +[job generate_files_3] /tmp/h7oc4fiq$ echo \ + 2 > /tmp/h7oc4fiq/output.txt Could not collect memory usage, job ended before monitoring began. [job generate_files_3] completed success [job generate_files_3] outputs { "output": { - "location": "file:///tmp/f1bl28mw/output.txt", + "location": "file:///tmp/h7oc4fiq/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3336,7 +3363,7 @@ [step generate_files] produced output { "file:///build/cwltool-3.0.20210124104916/tests/scatter_numbers.cwl#generate_files/output": [ { - "location": "file:///tmp/67d97vww/output.txt", + "location": "file:///tmp/k440iyvk/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3346,7 +3373,7 @@ "http://commonwl.org/cwltool#generation": 0 }, { - "location": "file:///tmp/ekpmrm8z/output.txt", + "location": "file:///tmp/jcuddu1e/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3356,7 +3383,7 @@ "http://commonwl.org/cwltool#generation": 0 }, { - "location": "file:///tmp/f1bl28mw/output.txt", + "location": "file:///tmp/h7oc4fiq/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3372,7 +3399,7 @@ [workflow _3] outputs { "output": [ { - "location": "file:///tmp/67d97vww/output.txt", + "location": "file:///tmp/k440iyvk/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3382,7 +3409,7 @@ "http://commonwl.org/cwltool#generation": 0 }, { - "location": "file:///tmp/ekpmrm8z/output.txt", + "location": "file:///tmp/jcuddu1e/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3392,7 +3419,7 @@ "http://commonwl.org/cwltool#generation": 0 }, { - "location": "file:///tmp/f1bl28mw/output.txt", + "location": "file:///tmp/h7oc4fiq/output.txt", "basename": "output.txt", "nameroot": "output", "nameext": ".txt", @@ -3403,17 +3430,17 @@ } ] } -[job generate_files_3] Removing input staging directory /tmp/jbh4hptc -[job generate_files_3] Removing temporary directory /tmp/ov6iza97 -Moving /tmp/67d97vww/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt -Moving /tmp/ekpmrm8z/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt_2 -Moving /tmp/f1bl28mw/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt_3 -Removing intermediate output directory /tmp/l1qedyg_ -Removing intermediate output directory /tmp/f1bl28mw -Removing intermediate output directory /tmp/ekpmrm8z -Removing intermediate output directory /tmp/67d97vww +[job generate_files_3] Removing input staging directory /tmp/r3rmm0u9 +[job generate_files_3] Removing temporary directory /tmp/vl9qxsbm +Moving /tmp/k440iyvk/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt +Moving /tmp/jcuddu1e/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt_2 +Moving /tmp/h7oc4fiq/output.txt to /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt_3 +Removing intermediate output directory /tmp/h7oc4fiq +Removing intermediate output directory /tmp/jcuddu1e +Removing intermediate output directory /tmp/kp6flj7e +Removing intermediate output directory /tmp/k440iyvk . -================= 315 passed, 103 skipped in 416.76s (0:06:56) ================= +================= 315 passed, 103 skipped in 364.19s (0:06:04) ================= I: pybuild pybuild:310: rm -Rf /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/tmp/ /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/main.cwl /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/output.txt* make[1]: Leaving directory '/build/cwltool-3.0.20210124104916' create-stamp debian/debhelper-build-stamp @@ -3461,16 +3488,16 @@ creating /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/__main__.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/factory.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/provenance.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/subgraph.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/provenance.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/pack.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/task_queue.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/executors.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/task_queue.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/cwlviewer.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/cwlrdf.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/resolver.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/argparser.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/workflow_job.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/resolver.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/provenance_profile.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/provenance_constants.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/checker.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ @@ -3478,12 +3505,12 @@ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/procgenerator.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/workflow.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/main.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/udocker.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/singularity.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/udocker.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/flatten.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/process.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/validate_js.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/update.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/process.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/job.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/docker_id.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/__pycache__/docker.cpython-39.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/__pycache__ @@ -3897,9 +3924,9 @@ creating /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests creating /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_validate_js.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_toolargparse.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_udocker.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_trs.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_toolargparse.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_tmpdir.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_target.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_subgraph.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ @@ -3912,13 +3939,13 @@ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_provenance.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_procgenerator.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_pathmapper.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_pack.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_parallel.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_pack.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_mpi.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_override.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_load_tool.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_js_sandbox.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_iwdr.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_js_sandbox.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_ext.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_http_input.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_fetch.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ @@ -3926,8 +3953,8 @@ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_empty_input.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_docker_warning.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_docker_paths_with_colons.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ -copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_docker.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_docker_info.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ +copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_docker.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_dependencies.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_default_path.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ copying /build/cwltool-3.0.20210124104916/.pybuild/cpython3_3.9_cwltool/build/cwltool/tests/__pycache__/test_cwl_version.cpython-39-pytest-6.0.2.pyc -> /build/cwltool-3.0.20210124104916/debian/cwltool/usr/lib/python3.9/dist-packages/cwltool/tests/__pycache__ @@ -4438,12 +4465,14 @@ 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/1815/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1815/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/23481 and its subdirectories -I: Current time: Fri May 31 08:42:19 -12 2024 -I: pbuilder-time-stamp: 1717188139 +I: removing directory /srv/workspace/pbuilder/1815 and its subdirectories +I: Current time: Sun Apr 30 04:28:15 +14 2023 +I: pbuilder-time-stamp: 1682778495