Diff of the two buildlogs: -- --- b1/build.log 2021-07-20 12:39:59.853378334 +0000 +++ b2/build.log 2021-07-20 12:46:57.501797637 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jul 20 00:36:33 -12 2021 -I: pbuilder-time-stamp: 1626784593 +I: Current time: Wed Jul 21 02:40:21 +14 2021 +I: pbuilder-time-stamp: 1626784821 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./iva_1.0.9+ds-11.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.nQsRACiw/trustedkeys.kbx': General error -gpgv: Signature made Mon Dec 21 22:23:23 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.F7D0zdEH/trustedkeys.kbx': General error +gpgv: Signature made Wed Dec 23 00:23:23 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ 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/5253/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/30465/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30465/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/30465/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,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='62306a7f98044e7a9370bdd374ebdda7' - 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='5253' - PS1='# ' - PS2='> ' + INVOCATION_ID=6999b724f7e648cc8bc163d08f11233a + 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=30465 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DTmST7jZtO/pbuilderrc_sEHB --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DTmST7jZtO/b1 --logfile b1/build.log iva_1.0.9+ds-11.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.DTmST7jZtO/pbuilderrc_8CwP --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.DTmST7jZtO/b2 --logfile b2/build.log --extrapackages usrmerge iva_1.0.9+ds-11.dsc' + SUDO_GID=114 + SUDO_UID=108 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux virt32b 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 16 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/5253/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 21 02:40 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 20 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/30465/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -355,7 +389,7 @@ Get: 123 http://deb.debian.org/debian bullseye/main armhf python3-pysam armhf 0.15.4+ds-3+b2 [1381 kB] Get: 124 http://deb.debian.org/debian bullseye/main armhf python3-setuptools all 52.0.0-4 [366 kB] Get: 125 http://deb.debian.org/debian bullseye/main armhf smalt armhf 0.7.6-9 [98.0 kB] -Fetched 257 MB in 26s (9792 kB/s) +Fetched 257 MB in 33s (7678 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -903,135 +937,135 @@ Setting up default-jdk-headless (2:1.11-72) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:Certigna.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:emSign_Root_CA_-_C1.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:Certigna_Root_CA.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem -Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:SecureTrust_CA.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:e-Szigno_Root_CA_2017.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:DST_Root_CA_X3.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:Certigna_Root_CA.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:AffirmTrust_Commercial.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:GTS_Root_R2.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:Comodo_AAA_Services_root.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:UCA_Global_G2_Root.pem +Adding debian:SecureTrust_CA.pem +Adding debian:QuoVadis_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Entrust_Root_Certification_Authority_-_G4.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:Izenpe.com.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Starfield_Class_2_CA.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:COMODO_ECC_Certification_Authority.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:GlobalSign_Root_CA_-_R3.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:Secure_Global_CA.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:GTS_Root_R4.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:GTS_Root_R3.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:emSign_Root_CA_-_G1.pem Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:EC-ACC.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:UCA_Extended_Validation_Root.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:Security_Communication_RootCA2.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:GTS_Root_R1.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Secure_Global_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Hongkong_Post_Root_CA_3.pem +Adding debian:emSign_Root_CA_-_C1.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:Certum_Trusted_Network_CA_2.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:GlobalSign_Root_CA_-_R2.pem +Adding debian:Security_Communication_Root_CA.pem Adding debian:Trustwave_Global_Certification_Authority.pem -Adding debian:GTS_Root_R3.pem -Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:Izenpe.com.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:Certigna.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:GTS_Root_R1.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:EC-ACC.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_1.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:UCA_Global_G2_Root.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:XRamp_Global_CA_Root.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:AffirmTrust_Premium.pem -Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem done. Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... @@ -1049,8 +1083,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (410 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 27228 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/iva-1.0.9+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_1.0.9+ds-11_source.changes +hostname: Name or service not known +I: Running cd /build/iva-1.0.9+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_1.0.9+ds-11_source.changes dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-11 dpkg-buildpackage: info: source distribution unstable @@ -1091,15 +1162,15 @@ chmod a+x scripts/* javac -verbose /build/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] -[parsing completed 151ms] +[parsing completed 365ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SizeFasta.java]] -[parsing completed 13ms] +[parsing completed 24ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] -[parsing completed 7ms] +[parsing completed 11ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/Utils.java]] -[parsing completed 46ms] +[parsing completed 73ms] [parsing started SimpleFileObject[/build/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] -[parsing completed 121ms] +[parsing completed 250ms] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.management/module-info.class] @@ -1270,7 +1341,7 @@ [checking getScaffoldStats] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class] [wrote /build/iva-1.0.9+ds/iva/gage/getScaffoldStats.class] -[total 4646ms] +[total 9504ms] dh_auto_build -- I: pybuild base:232: /usr/bin/python3 setup.py build Checking dependencies found in path: @@ -1284,71 +1355,71 @@ running build running build_py creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/qc.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/contig_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/kcount.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/external_progs.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/seed_processor.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/contig.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/egg_extract.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/graph.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/seed.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/qc.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/mummer.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/edge.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/assembly.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/seed_processor.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/kcount.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/kraken.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/test_data_runner.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/__init__.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/external_progs.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/kmers.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/edge.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/mapping.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/common.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/kraken.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/qc_external.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/seed.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/graph.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva +copying iva/kmers.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva copying iva/read_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/mapping.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/test_data_runner.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/mummer.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva -copying iva/contig_trim.py -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/colsum.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/Utils.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/colsum.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage -copying iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage +copying iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt +copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt -copying iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/ratt.config -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt -copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt +copying iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt -copying iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt +copying iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim creating /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data -copying iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data -copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data -copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data +copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data +copying iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data +copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.9 -copying and adjusting scripts/iva_qc -> build/scripts-3.9 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.9 copying and adjusting scripts/iva -> build/scripts-3.9 -changing mode of build/scripts-3.9/iva_qc from 644 to 755 +copying and adjusting scripts/iva_qc -> build/scripts-3.9 changing mode of build/scripts-3.9/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.9/iva from 644 to 755 +changing mode of build/scripts-3.9/iva_qc from 644 to 755 make[1]: Leaving directory '/build/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iva-1.0.9+ds' @@ -1436,9 +1507,9 @@ [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.2.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.3.3.map.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.4.1.map.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.filter_reads.pqvig_ci/out.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.filter_reads.lint9y40/out.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.extend.1.5.1.map.bam' -[E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.trim_strand_biased_ends.zuv5woi5/out.unsorted.bam' +[E::idx_find_and_load] Could not retrieve index file for '/build/iva-1.0.9+ds/tmp.trim_strand_biased_ends.cwck6aok/out.unsorted.bam' ok test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok @@ -1744,7 +1815,7 @@ Test write_fasta ... ok ---------------------------------------------------------------------- -Ran 160 tests in 18.407s +Ran 160 tests in 31.452s OK make[1]: Leaving directory '/build/iva-1.0.9+ds' @@ -1771,82 +1842,82 @@ creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9 creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kcount.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/external_progs.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed_processor.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/egg_extract.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/graph.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/assembly.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed_processor.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mummer.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/main.ratt.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/genbank2embl.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/embl2gff.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/start.ratt.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt.config.hiv -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kcount.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/__init__.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/external_progs.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kmers.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/ratt/ratt_correction.pm -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/ratt copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/edge.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/assembly.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kraken.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_data_runner.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/__init__.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mapping.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/common.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc_external.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/seed.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_2.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reference.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/common.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kraken.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/qc_external.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/reads_1.fq.gz -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_run_data +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/graph.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/kmers.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mapping.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getMummerStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$ToProtein.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Translate.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getCorrectnessStats.sh -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/colsum.pl -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SplitFastaByLetter.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/getScaffoldStats.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/SizeFasta.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/GetFastaStats.java -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/gage/Utils$Pair.class -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/gage -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/test_data_runner.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/mummer.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/contig_trim.py -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc.py to qc.cpython-39.pyc +creating /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim +copying /build/iva-1.0.9+ds/.pybuild/cpython3_3.9_iva/build/iva/read_trim/adapters.fasta -> /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig_trim.py to contig_trim.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kcount.py to kcount.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/external_progs.py to external_progs.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed_processor.py to seed_processor.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig.py to contig.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/egg_extract.py to egg_extract.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/graph.py to graph.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed.py to seed.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc.py to qc.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mummer.py to mummer.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/edge.py to edge.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/assembly.py to assembly.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed_processor.py to seed_processor.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kcount.py to kcount.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kraken.py to kraken.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/__init__.py to __init__.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/external_progs.py to external_progs.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kmers.py to kmers.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/edge.py to edge.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mapping.py to mapping.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/common.py to common.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kraken.py to kraken.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/qc_external.py to qc_external.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/seed.py to seed.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/graph.py to graph.cpython-39.pyc +byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/kmers.py to kmers.cpython-39.pyc byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/read_trim.py to read_trim.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mapping.py to mapping.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/mummer.py to mummer.cpython-39.pyc -byte-compiling /build/iva-1.0.9+ds/debian/iva/usr/lib/python3.9/dist-packages/iva/contig_trim.py to contig_trim.cpython-39.pyc running install_egg_info running egg_info writing iva.egg-info/PKG-INFO @@ -1859,12 +1930,12 @@ Skipping SOURCES.txt running install_scripts creating /build/iva-1.0.9+ds/debian/iva/usr/bin -copying build/scripts-3.9/iva_qc -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva_qc_make_db -> /build/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.9/iva -> /build/iva-1.0.9+ds/debian/iva/usr/bin -changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755 +copying build/scripts-3.9/iva_qc -> /build/iva-1.0.9+ds/debian/iva/usr/bin changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva to 755 +changing mode of /build/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman @@ -1905,12 +1976,14 @@ 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/30465/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30465/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/5253 and its subdirectories -I: Current time: Tue Jul 20 00:39:56 -12 2021 -I: pbuilder-time-stamp: 1626784796 +I: removing directory /srv/workspace/pbuilder/30465 and its subdirectories +I: Current time: Wed Jul 21 02:46:52 +14 2021 +I: pbuilder-time-stamp: 1626785212