Diff of the two buildlogs: -- --- b1/build.log 2023-05-01 14:12:34.551389585 +0000 +++ b2/build.log 2023-05-01 14:21:59.698614941 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 1 02:06:03 -12 2023 -I: pbuilder-time-stamp: 1682949963 +I: Current time: Mon Jun 3 10:35:38 +14 2024 +I: pbuilder-time-stamp: 1717360538 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./python-pbcore_2.1.2+dfsg.orig.tar.xz] I: copying [./python-pbcore_2.1.2+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 7 03:59:55 2023 -12 +gpgv: Signature made Sun Jan 8 05:59:55 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,167 @@ dpkg-source: info: applying numpy_1.24.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3095761/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3498304/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 3 10:36 /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/3498304/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3498304/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='670c570f258f40aca927e3fc15ad72a7' - 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='3095761' - PS1='# ' - PS2='> ' + INVOCATION_ID=345d68895f3948b585d69179a0ed2e87 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3498304 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.gohQ7iCB/pbuilderrc_ujMa --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gohQ7iCB/b1 --logfile b1/build.log python-pbcore_2.1.2+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.gohQ7iCB/pbuilderrc_OPVv --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gohQ7iCB/b2 --logfile b2/build.log --extrapackages usrmerge python-pbcore_2.1.2+dfsg-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3095761/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 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 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 3 10:36 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 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 6460 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 8103 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/3498304/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -398,7 +430,7 @@ Get: 168 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 python3-uritools all 4.0.0-1 [25.3 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 python3-xmlschema all 1.10.0-6 [177 kB] -Fetched 74.8 MB in 3s (29.4 MB/s) +Fetched 74.8 MB in 2s (33.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (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 ... 19596 files and directories currently installed.) @@ -1109,8 +1141,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/python-pbcore-2.1.2+dfsg/ && 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 > ../python-pbcore_2.1.2+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/3498304/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3498304/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/python-pbcore-2.1.2+dfsg/ && 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 > ../python-pbcore_2.1.2+dfsg-5_source.changes dpkg-buildpackage: info: source package python-pbcore dpkg-buildpackage: info: source version 2.1.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -1347,7 +1390,7 @@ making output directory... done loading intersphinx inventory from http://docs.python.org/objects.inv... WARNING: failed to reach any of the inventories with the following issues: -intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) +intersphinx inventory 'http://docs.python.org/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date building [html]: targets for 11 source files that are out of date updating environment: [new config] 11 added, 0 changed, 0 removed @@ -1443,7 +1486,7 @@ cachedir: .pytest_cache rootdir: /build/python-pbcore-2.1.2+dfsg, configfile: pytest.ini plugins: xdist-3.1.0, cov-4.0.0 -gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I / gw8 I / gw9 I / gw10 I / gw11 I / gw12 I / gw13 I / gw14 I +gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I / gw8 I / gw9 I / gw10 I / gw11 I / gw12 I / gw13 I / gw14 I / gw15 I [gw0] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw1] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw2] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg @@ -1459,268 +1502,270 @@ [gw12] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw13] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg [gw14] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg + [gw15] linux Python 3.11.2 cwd: /build/python-pbcore-2.1.2+dfsg + [gw3] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw4] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw0] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw1] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw2] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw3] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw5] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw4] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw8] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw6] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw7] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw5] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw9] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw12] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw8] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw7] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw14] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw10] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] + [gw15] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw11] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] [gw13] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] - [gw14] Python 3.11.2 (main, Mar 13 2023, 12:18:29) [GCC 12.2.0] -gw0 [140] / gw1 [140] / gw2 [140] / gw3 [140] / gw4 [140] / gw5 [140] / gw6 [140] / gw7 [140] / gw8 [140] / gw9 [140] / gw10 [140] / gw11 [140] / gw12 [140] / gw13 [140] / gw14 [140] +gw0 [140] / gw1 [140] / gw2 [140] / gw3 [140] / gw4 [140] / gw5 [140] / gw6 [140] / gw7 [140] / gw8 [140] / gw9 [140] / gw10 [140] / gw11 [140] / gw12 [140] / gw13 [140] / gw14 [140] / gw15 [140] scheduling tests via LoadScopeScheduling tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ -tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations -[gw5] [ 0%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations -tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties -tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range -[gw6] [ 1%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties +tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations -[gw7] [ 2%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties -tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +tests/test_pbcore_io_BlasrIO.py::test_m4 +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration +tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations +tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties +tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta -[gw11] [ 2%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ -[gw11] [ 3%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ -tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam -[gw12] [ 4%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam -tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader -[gw12] [ 5%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader -[gw6] [ 5%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names -tests/test_pbcore_io_FofnIO.py::test_simple -tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str -[gw7] [ 6%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str -tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable -[gw13] [ 7%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString -[gw11] [ 7%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString -tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support -[gw4] [ 8%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support -tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 -[gw4] [ 9%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 -[gw8] [ 10%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 -[gw8] [ 10%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 -[gw5] [ 11%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 -tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 -[gw14] [ 12%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 +[gw6] [ 0%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestTranscriptBam::test_transcript_set_support +tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping +[gw10] [ 1%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__init__ +tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range +[gw15] [ 2%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_readFasta +[gw12] [ 2%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMissingHeaderM5::test_retrieve_read_group_properties +tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers +[gw11] [ 3%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta1 tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 -[gw14] [ 12%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 -[gw3] [ 13%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations -tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement -[gw1] [ 14%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement -tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs -[gw1] [ 15%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs -[gw13] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation +tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta +[gw2] [ 4%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testBasicOperations +tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable +[gw12] [ 5%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers +[gw9] [ 5%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties +tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names +[gw4] [ 6%] PASSED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ -[gw5] [ 16%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ +[gw8] [ 7%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping +tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader +[gw8] [ 7%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeHeader +[gw14] [ 8%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 +tests/test_pbcore_io_BlasrIO.py::test_m5 +[gw14] [ 9%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 +[gw11] [ 10%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaWriter::test_writeFasta2 +[gw4] [ 10%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__init__ tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ -[gw5] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString -[gw5] [ 17%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 -[gw11] [ 18%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 -[gw11] [ 19%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len -[gw11] [ 20%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq -[gw11] [ 20%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq -[gw3] [ 21%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName -[gw5] [ 22%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 -[gw3] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName -[gw5] [ 23%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead -tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification -[gw7] [ 24%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification -tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString -[gw7] [ 25%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString -[gw6] [ 25%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple +tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations +[gw9] [ 11%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_sample_names +tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str +[gw5] [ 12%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestEmptyBam::test_empty_bam_reads_in_range +tests/test_pbcore_io_FofnIO.py::test_simple +[gw5] [ 12%] PASSED tests/test_pbcore_io_FofnIO.py::test_simple tests/test_pbcore_io_FofnIO.py::test_empty_lines -[gw6] [ 26%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines tests/test_dataset_run_split.py::test -[gw0] [ 27%] SKIPPED tests/test_dataset_run_split.py::test -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration -[gw0] [ 27%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration +[gw3] [ 13%] SKIPPED tests/test_dataset_run_split.py::test +tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs +[gw3] [ 14%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ +[gw10] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test__str__ +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString +[gw10] [ 15%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_fromString +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 +[gw5] [ 16%] PASSED tests/test_pbcore_io_FofnIO.py::test_empty_lines +[gw9] [ 17%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_str +[gw15] [ 17%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta +tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification +[gw11] [ 18%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations +[gw13] [ 19%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testIteration tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName -[gw0] [ 28%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName +[gw13] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByName tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById -[gw0] [ 29%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById +[gw13] [ 20%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessById tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition -[gw0] [ 30%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition +[gw13] [ 21%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testAccessByPosition tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice -[gw0] [ 30%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice +[gw13] [ 22%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::testSlice +[gw1] [ 22%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation +[gw1] [ 23%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testStrandOrientation +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName +[gw1] [ 24%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadName +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead +[gw1] [ 25%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 +[gw6] [ 25%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 +[gw6] [ 26%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -tests/test_pbcore_io_BlasrIO.py::test_m4 -[gw10] [ 31%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m4 -tests/test_pbcore_io_BlasrIO.py::test_m5 -[gw10] [ 32%] PASSED tests/test_pbcore_io_BlasrIO.py::test_m5 +tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ +[gw12] [ 27%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ +tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord +[gw8] [ 27%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord +tests/test_pbdataset_split.py::TestDataSetSplit::test_split +[gw4] [ 28%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString +[gw4] [ 29%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_fromString +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 +[gw4] [ 30%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead +[gw1] [ 30%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference +[gw1] [ 31%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 +[gw4] [ 32%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 +tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam +[gw2] [ 32%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestCCSBam::testQStartEndUnavailable +tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 +[gw2] [ 33%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq1 +[gw7] [ 34%] SKIPPED tests/test_pbcore_io_AlnFileReaders.py::TestBarcodedBam::test_read_lima_demultiplexed_bam tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs -[gw10] [ 32%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs +[gw7] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted -[gw10] [ 33%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted +[gw7] [ 35%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_merge_gffs_sorted tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff -[gw10] [ 34%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff +[gw7] [ 36%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_sort_gff +[gw0] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len -[gw5] [ 35%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len +[gw4] [ 37%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_len tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq -[gw5] [ 35%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq -[gw2] [ 36%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations +[gw4] [ 38%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_eq +tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 +[gw15] [ 39%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse +[gw15] [ 40%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement +[gw9] [ 40%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_modification +tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString +[gw9] [ 41%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_fromString tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation -[gw2] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation +[gw13] [ 42%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta +[gw15] [ 42%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement +[gw15] [ 43%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac +[gw15] [ 44%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error +tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted +[gw14] [ 45%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted +tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference +[gw1] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV +[gw1] [ 46%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript +[gw12] [ 47%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv +[gw10] [ 47%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement1 +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 +[gw10] [ 48%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_reverse_complement2 +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len +[gw10] [ 49%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_len +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq +[gw10] [ 50%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_eq +[gw0] [ 50%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testStrandOrientation tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName -[gw2] [ 37%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName +[gw0] [ 51%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadName tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead -[gw2] [ 38%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead +[gw0] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead -[gw2] [ 39%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead +[gw0] [ 52%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead +[gw1] [ 53%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments +[gw1] [ 54%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference -[gw2] [ 40%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference -tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord -[gw12] [ 40%] PASSED tests/test_pbcore_io_GffIO.py::TestGffWriter::test_writeRecord -tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations -[gw12] [ 41%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testInvalidOperations -[gw3] [ 42%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead -[gw3] [ 42%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference -[gw3] [ 43%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference -[gw3] [ 44%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV -[gw8] [ 45%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 +[gw0] [ 55%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference +[gw15] [ 55%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference -[gw2] [ 45%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference -tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV -tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted -[gw13] [ 46%] PASSED tests/test_pbcore_io_VcfIO.py::TestVcfSorting::test_merge_vcfs_sorted -tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv -[gw13] [ 47%] PASSED tests/test_pbcore_util.py::TestStatistics::test_accuracy_as_phred_qv -[gw3] [ 47%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testDeletionQV -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript -[gw0] [ 48%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -[gw3] [ 49%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript -tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping -[gw9] [ 50%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestUpdatedChemistryMapping::test_load_updated_mapping -tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers -[gw9] [ 50%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test_headers -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments -[gw3] [ 51%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments -tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 -[gw8] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 -tests/test_pbdataset_split.py::TestDataSetSplit::test_split -tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 -[gw4] [ 52%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse -[gw4] [ 53%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement -[gw4] [ 54%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement -tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal -[gw5] [ 55%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal +[gw0] [ 56%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedReference tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange -[gw2] [ 55%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV -[gw4] [ 56%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverseComplement -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac -[gw4] [ 57%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_iupac -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error -[gw4] [ 57%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_complement_error -tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal -[gw11] [ 58%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal -tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 -[gw14] [ 59%] SKIPPED tests/test_pbcore_io_lossless_bam.py::TestCase::test_1 -tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid -[gw14] [ 60%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid -tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype -tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii -[gw1] [ 60%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii +tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd +[gw11] [ 57%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency -tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy -[gw13] [ 61%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy -tests/test_pbcore_io_FofnIO.py::test_absolutifying -[gw6] [ 62%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying +tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal +[gw4] [ 57%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_not_equal tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get -[gw7] [ 62%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get -[gw14] [ 63%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype -tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV +[gw0] [ 58%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testDeletionQV +[gw14] [ 59%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +[gw9] [ 60%] PASSED tests/test_pbcore_io_GffIO.py::TestGff3Record::test_get tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript -[gw2] [ 64%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript +[gw0] [ 60%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments -[gw2] [ 65%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments +[gw0] [ 61%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii +tests/test_pbcore_io_FofnIO.py::test_absolutifying +[gw5] [ 62%] PASSED tests/test_pbcore_io_FofnIO.py::test_absolutifying +[gw3] [ 62%] PASSED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testQvsFromAscii +tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error +[gw15] [ 63%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error +tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal +[gw10] [ 64%] PASSED tests/test_pbcore_io_FastaIO.py::TestFastaRecord::test_not_equal +tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex +[gw13] [ 65%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex +tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy +[gw12] [ 65%] PASSED tests/test_pbcore_util.py::TestStatistics::test_phred_qv_as_accuracy +tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype +tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 +[gw2] [ 66%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqReader::test_readFastq2 +tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 +[gw6] [ 67%] PASSED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file -[gw14] [ 65%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix -tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd -[gw12] [ 66%] PASSED tests/test_pbcore_io_unaligned_bam.py::TestUnalignedBam::testIpd -[gw1] [ 67%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +[gw7] [ 67%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file +[gw14] [ 68%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype +tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +[gw14] [ 69%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_dsIdToSuffix +tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges +[gw11] [ 70%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming -[gw1] [ 67%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming +[gw14] [ 70%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges +[gw11] [ 71%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire -tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex -[gw0] [ 68%] PASSED tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_readWeirdFastaIndex -tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges -[gw14] [ 69%] PASSED tests/test_pbdataset_utils.py::TestDataSetUtils::test_divideKeys_keysToRanges -tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error -[gw4] [ 70%] PASSED tests/test_pbcore_util_sequences.py::TestReverseComplement::test_reverse_complement_error -[gw1] [ 70%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire +[gw11] [ 72%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_streaming_entire tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index -[gw1] [ 71%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index -tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ -[gw9] [ 72%] PASSED tests/test_pbcore_io_GffIO.py::TestGffReader::test__iter__ -[gw10] [ 72%] PASSED tests/test_pbcore_io_GffIO.py::TestGffSorting::test_empty_file +[gw11] [ 72%] PASSED tests/test_pbindex.py::TestPbIndex::test_pbindex_with_zmw_index [gw8] [ 73%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws -[gw3] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange +[gw1] [ 74%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable -[gw3] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable +[gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry -[gw3] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry +[gw1] [ 75%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV -[gw3] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV +[gw1] [ 76%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testMapQV tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -[gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts -[gw3] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName -[gw3] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam -[gw3] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity -[gw3] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity -tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed -[gw2] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +[gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable -[gw2] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable +[gw0] [ 77%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadGroupTable tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry -[gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry +[gw0] [ 78%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSequencingChemistry tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion -[gw2] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion +[gw0] [ 79%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testSpecVersion tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore -[gw2] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore +[gw0] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadScore tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default -[gw3] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed -[gw2] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default +[gw0] [ 80%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_sample_name_default +[gw1] [ 81%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts +[gw1] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default -[gw2] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default -[gw8] [ 86%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws +[gw0] [ 82%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::test_library_name_default +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName +[gw1] [ 83%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam +[gw1] [ 84%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_empty_bam +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +[gw1] [ 85%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +[gw8] [ 85%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws +tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize +[gw1] [ 86%] PASSED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed [gw8] [ 87%] PASSED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws [gw8] [ 87%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_large_split_zmws @@ -1760,15 +1805,15 @@ [gw8] [100%] SKIPPED tests/test_pbdataset_split.py::TestDataSetSplit::test_split_read_groups =============================== warnings summary =============================== -tests/test_pbcore_io_FastqIO.py: 11 warnings - /build/python-pbcore-2.1.2+dfsg/pbcore/io/FastqIO.py:239: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. - return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("ascii") - tests/test_pbcore_extract_bam_sequence.py: 1 warning tests/test_pbcore_io_AlnFileReaders.py: 118 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:356: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return _gusfieldTrans[uc].tostring().decode("ascii") +tests/test_pbcore_io_FastqIO.py: 11 warnings + /build/python-pbcore-2.1.2+dfsg/pbcore/io/FastqIO.py:239: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. + return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("ascii") + tests/test_pbcore_io_AlnFileReaders.py: 28 warnings /build/python-pbcore-2.1.2+dfsg/pbcore/io/align/BamAlignment.py:583: DeprecationWarning: tostring() is deprecated. Use tobytes() instead. return r.tostring().decode("ascii") @@ -1812,27 +1857,27 @@ Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= -0.71s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks -0.70s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange -0.57s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split -0.47s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws -0.45s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange -0.41s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split -0.37s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize -0.35s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split -0.15s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency -0.13s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed -0.11s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations -0.10s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations -0.08s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta -0.07s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows -0.07s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +1.11s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split +1.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks +0.95s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize +0.81s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange +0.78s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange +0.69s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split +0.56s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws +0.37s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split +0.26s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed +0.25s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency +0.23s teardown tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid +0.14s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity +0.10s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta +0.09s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows +0.09s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations +0.09s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers +0.08s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations +0.08s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name -0.04s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers -0.04s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta -0.04s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid -0.03s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_metatype -================ 122 passed, 18 skipped, 212 warnings in 13.91s ================ +0.05s call tests/test_pbcore_io_FastaIO.py::TestFastaReader::test_dosLineEndingsFasta +================ 122 passed, 18 skipped, 212 warnings in 18.02s ================ # copy working test data into doc dir as user examples mkdir -p _tmp/usr/share/doc/python3-pbcore cp -a tests _tmp/usr/share/doc/python3-pbcore @@ -2386,8 +2431,8 @@ dpkg-gencontrol: warning: Depends field of package python-pbcore-doc: substitution variable ${sphinxdoc:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pbcore' in '../python3-pbcore_2.1.2+dfsg-5_all.deb'. dpkg-deb: building package 'python-pbcore-doc' in '../python-pbcore-doc_2.1.2+dfsg-5_all.deb'. +dpkg-deb: building package 'python3-pbcore' in '../python3-pbcore_2.1.2+dfsg-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pbcore_2.1.2+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pbcore_2.1.2+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2395,12 +2440,14 @@ 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/3498304/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3498304/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/3095761 and its subdirectories -I: Current time: Mon May 1 02:12:34 -12 2023 -I: pbuilder-time-stamp: 1682950354 +I: removing directory /srv/workspace/pbuilder/3498304 and its subdirectories +I: Current time: Mon Jun 3 10:44:59 +14 2024 +I: pbuilder-time-stamp: 1717361099