Diff of the two buildlogs:
--
--- b1/build.log 2023-06-08 15:16:31.378474475 +0000
+++ b2/build.log 2023-06-08 15:27:39.585272745 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Thu Jun 8 03:11:38 -12 2023
-I: pbuilder-time-stamp: 1686237098
+I: Current time: Fri Jun 9 05:17:24 +14 2023
+I: pbuilder-time-stamp: 1686237444
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 [./iva_1.0.11+ds.orig.tar.xz]
I: copying [./iva_1.0.11+ds-3.debian.tar.xz]
I: Extracting source
-gpgv: Signature made Fri Dec 2 05:12:51 2022 -12
+gpgv: Signature made Sat Dec 3 07:12:51 2022 +14
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
@@ -31,135 +31,167 @@
dpkg-source: info: applying disable-ram-test.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/4922/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/30498/tmp/hooks/D01_modify_environment starting
+debug: Running on wbq0.
+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 9 05:19 /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/30498/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/30498/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='armhf'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 '
- DISTRIBUTION='bookworm'
- HOME='/root'
- HOST_ARCH='armhf'
+ 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]="arm-unknown-linux-gnueabihf")
+ 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=armhf
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
+ DIRSTACK=()
+ DISTRIBUTION=bookworm
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=arm
+ HOST_ARCH=armhf
IFS='
'
- INVOCATION_ID='09518d2cfa654256a534bf2be4282cc9'
- 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='4922'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=478656f406064e0eb9b5724e1d83c71e
+ LANG=C
+ LANGUAGE=it_CH:it
+ LC_ALL=C
+ MACHTYPE=arm-unknown-linux-gnueabihf
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnueabihf
+ 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=30498
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.cxrMuTHm/pbuilderrc_wjyb --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.cxrMuTHm/b1 --logfile b1/build.log iva_1.0.11+ds-3.dsc'
- SUDO_GID='114'
- SUDO_UID='110'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://10.0.0.15:3142/'
+ 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.cxrMuTHm/pbuilderrc_NUlR --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.cxrMuTHm/b2 --logfile b2/build.log --extrapackages usrmerge iva_1.0.11+ds-3.dsc'
+ SUDO_GID=113
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://10.0.0.15:3142/
I: uname -a
- Linux jtx1b 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux
I: ls -l /bin
total 5072
- -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
- -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
- -rwxr-xr-x 3 root root 67144 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 67144 Sep 18 2022 bzip2
- -rwxr-xr-x 1 root root 67112 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 67632 Sep 20 2022 cat
- -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
- -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
- -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
- -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
- -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
- -rwxr-xr-x 1 root root 133220 Sep 20 2022 date
- -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
- -rwxr-xr-x 1 root root 68104 Sep 20 2022 df
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
- -rwxr-xr-x 1 root root 59128 Mar 22 21:02 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 67560 Sep 20 2022 echo
- -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
- -rwxr-xr-x 1 root root 67548 Sep 20 2022 false
- -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
- -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
- -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
- -rwxr-xr-x 1 root root 128608 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 64220 Apr 9 2022 gzip
- -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
- -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
- -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
- -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
- -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
- -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
- -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
- -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
- -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
- -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
- -rwxr-xr-x 1 root root 133532 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 67608 Sep 20 2022 pwd
- lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
- -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
- -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
- -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
- -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
- -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
- lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
- -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
- -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
- -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
- -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
- -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
- -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
- -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
- -rwxr-xr-x 1 root root 67548 Sep 20 2022 true
- -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
- -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
- -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
- -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
- -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
- -rwxr-xr-x 1 root root 42608 Mar 22 21:02 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/4922/tmp/hooks/D02_print_environment finished
+ -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash
+ -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2
+ -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2
+ -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat
+ -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp
+ -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod
+ -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown
+ -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp
+ -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash
+ -rwxr-xr-x 1 root root 133220 Sep 21 2022 date
+ -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd
+ -rwxr-xr-x 1 root root 68104 Sep 21 2022 df
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir
+ -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
+ -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo
+ -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
+ -rwxr-xr-x 1 root root 67548 Sep 21 2022 false
+ -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
+ -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt
+ -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount
+ -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip
+ -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname
+ -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln
+ -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls
+ -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk
+ -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir
+ -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod
+ -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp
+ -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more
+ -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount
+ -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint
+ -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd
+ lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
+ -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink
+ -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm
+ -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir
+ -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts
+ -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed
+ lrwxrwxrwx 1 root root 9 Jun 9 05:19 sh -> /bin/bash
+ -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep
+ -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty
+ -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su
+ -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync
+ -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar
+ -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile
+ -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch
+ -rwxr-xr-x 1 root root 67548 Sep 21 2022 true
+ -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server
+ -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount
+ -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname
+ -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
+ -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir
+ -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl
+ lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/30498/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -356,7 +388,7 @@
Get: 125 http://deb.debian.org/debian bookworm/main armhf python3-pytest all 7.2.1-2 [236 kB]
Get: 126 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB]
Get: 127 http://deb.debian.org/debian bookworm/main armhf smalt armhf 0.7.6-12 [98.4 kB]
-Fetched 268 MB in 25s (10.7 MB/s)
+Fetched 268 MB in 43s (6286 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package readline-common.
(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 ... 19324 files and directories currently installed.)
@@ -1062,8 +1094,19 @@
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/iva-1.0.11+ds/ && 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 > ../iva_1.0.11+ds-3_source.changes
+I: user script /srv/workspace/pbuilder/30498/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/30498/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/iva-1.0.11+ds/ && 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 > ../iva_1.0.11+ds-3_source.changes
dpkg-buildpackage: info: source package iva
dpkg-buildpackage: info: source version 1.0.11+ds-3
dpkg-buildpackage: info: source distribution unstable
@@ -1104,15 +1147,15 @@
chmod a+x scripts/*
javac -verbose /build/iva-1.0.11+ds/iva/gage/*.java
[parsing started SimpleFileObject[/build/iva-1.0.11+ds/iva/gage/GetFastaStats.java]]
-[parsing completed 161ms]
+[parsing completed 709ms]
[parsing started SimpleFileObject[/build/iva-1.0.11+ds/iva/gage/SizeFasta.java]]
-[parsing completed 17ms]
+[parsing completed 73ms]
[parsing started SimpleFileObject[/build/iva-1.0.11+ds/iva/gage/SplitFastaByLetter.java]]
-[parsing completed 10ms]
+[parsing completed 60ms]
[parsing started SimpleFileObject[/build/iva-1.0.11+ds/iva/gage/Utils.java]]
-[parsing completed 40ms]
+[parsing completed 403ms]
[parsing started SimpleFileObject[/build/iva-1.0.11+ds/iva/gage/getScaffoldStats.java]]
-[parsing completed 82ms]
+[parsing completed 564ms]
[loading /modules/jdk.crypto.ec/module-info.class]
[loading /modules/java.net.http/module-info.class]
[loading /modules/jdk.jartool/module-info.class]
@@ -1290,7 +1333,7 @@
[checking getScaffoldStats]
[wrote /build/iva-1.0.11+ds/iva/gage/getScaffoldStats$Scaffold.class]
[wrote /build/iva-1.0.11+ds/iva/gage/getScaffoldStats.class]
-[total 3966ms]
+[total 17022ms]
dh_auto_build --
I: pybuild base:240: /usr/bin/python3 setup.py build
Checking dependencies found in path:
@@ -1304,71 +1347,71 @@
running build
running build_py
creating /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/__init__.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/egg_extract.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/mapping.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/test_data_runner.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/kraken.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/seed.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/contig.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/kmers.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/external_progs.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/contig_trim.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/seed_processor.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/read_trim.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/kraken.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/mapping.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/mummer.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/seed_processor.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/edge.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/egg_extract.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/kmers.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/contig.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/kcount.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/common.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/qc_external.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
-copying iva/graph.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/__init__.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/edge.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/assembly.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/graph.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/common.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
copying iva/qc.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/qc_external.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/contig_trim.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
+copying iva/seed.py -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva
creating /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getScaffoldStats.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/SizeFasta.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/Utils$Pair.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/SizeFasta.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/GetFastaStats.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/Utils$ToProtein.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/colsum.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/SizeFasta.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/Utils$ToProtein.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/Utils$Pair.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/SizeFasta.java -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/colsum.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
+copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/getMummerStats.sh -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
-copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/GetFastaStats.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
copying iva/gage/Utils$Translate.class -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage
creating /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
-copying iva/ratt/genbank2embl.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
+copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
+copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
+copying iva/ratt/main.ratt.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/embl2gff.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
+copying iva/ratt/genbank2embl.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/start.ratt.sh -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
-copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
copying iva/ratt/ratt.config -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
-copying iva/ratt/main.ratt.pl -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
-copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt
creating /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim
copying iva/read_trim/adapters.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim
creating /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
-copying iva/test_run_data/reference.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
-copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
-copying iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
-copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
+copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
+copying iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
+copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
copying iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
+copying iva/test_run_data/reference.fasta -> /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data
running build_scripts
creating build
creating build/scripts-3.11
copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.11
-copying and adjusting scripts/iva_qc -> build/scripts-3.11
copying and adjusting scripts/iva -> build/scripts-3.11
+copying and adjusting scripts/iva_qc -> build/scripts-3.11
changing mode of build/scripts-3.11/iva_qc_make_db from 644 to 755
-changing mode of build/scripts-3.11/iva_qc from 644 to 755
changing mode of build/scripts-3.11/iva from 644 to 755
+changing mode of build/scripts-3.11/iva_qc from 644 to 755
make[1]: Leaving directory '/build/iva-1.0.11+ds'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/iva-1.0.11+ds'
@@ -1578,7 +1621,7 @@
class Tester:
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-======================= 160 passed, 9 warnings in 12.46s =======================
+======================= 160 passed, 9 warnings in 34.08s =======================
make[1]: Leaving directory '/build/iva-1.0.11+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
@@ -1605,82 +1648,82 @@
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/__init__.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/egg_extract.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mapping.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_data_runner.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kraken.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kmers.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/external_progs.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig_trim.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/main.ratt.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/embl2gff.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/start.ratt.sh -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/main.ratt.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/ratt
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_data_runner.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/external_progs.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed_processor.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kraken.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/getMummerStats.sh -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/GetFastaStats.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/gage/Utils$Translate.class -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/gage
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mapping.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/mummer.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed_processor.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/egg_extract.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kmers.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kcount.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/__init__.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/edge.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/assembly.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/graph.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
creating /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reference.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/kcount.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/test_run_data/reference.fasta -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_run_data
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/common.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc_external.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/graph.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/assembly.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/__init__.py to __init__.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/egg_extract.py to egg_extract.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mapping.py to mapping.cpython-311.pyc
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/qc_external.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/contig_trim.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
+copying /build/iva-1.0.11+ds/.pybuild/cpython3_3.11_iva/build/iva/seed.py -> /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kraken.py to kraken.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed.py to seed.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig.py to contig.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kmers.py to kmers.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/external_progs.py to external_progs.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig_trim.py to contig_trim.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed_processor.py to seed_processor.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/read_trim.py to read_trim.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kraken.py to kraken.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mapping.py to mapping.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/mummer.py to mummer.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed_processor.py to seed_processor.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/edge.py to edge.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/egg_extract.py to egg_extract.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kmers.py to kmers.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig.py to contig.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/kcount.py to kcount.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/common.py to common.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc_external.py to qc_external.cpython-311.pyc
-byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/graph.py to graph.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/__init__.py to __init__.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/edge.py to edge.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/assembly.py to assembly.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/graph.py to graph.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/common.py to common.cpython-311.pyc
byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc.py to qc.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/qc_external.py to qc_external.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/contig_trim.py to contig_trim.cpython-311.pyc
+byte-compiling /build/iva-1.0.11+ds/debian/iva/usr/lib/python3.11/dist-packages/iva/seed.py to seed.cpython-311.pyc
running install_egg_info
running egg_info
creating iva.egg-info
@@ -1698,11 +1741,11 @@
running install_scripts
creating /build/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.11/iva_qc_make_db -> /build/iva-1.0.11+ds/debian/iva/usr/bin
-copying build/scripts-3.11/iva_qc -> /build/iva-1.0.11+ds/debian/iva/usr/bin
copying build/scripts-3.11/iva -> /build/iva-1.0.11+ds/debian/iva/usr/bin
+copying build/scripts-3.11/iva_qc -> /build/iva-1.0.11+ds/debian/iva/usr/bin
changing mode of /build/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc_make_db to 755
-changing mode of /build/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755
changing mode of /build/iva-1.0.11+ds/debian/iva/usr/bin/iva to 755
+changing mode of /build/iva-1.0.11+ds/debian/iva/usr/bin/iva_qc to 755
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
debian/rules override_dh_installman
@@ -1743,12 +1786,14 @@
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/30498/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/30498/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/4922 and its subdirectories
-I: Current time: Thu Jun 8 03:16:25 -12 2023
-I: pbuilder-time-stamp: 1686237385
+I: removing directory /srv/workspace/pbuilder/30498 and its subdirectories
+I: Current time: Fri Jun 9 05:27:35 +14 2023
+I: pbuilder-time-stamp: 1686238055