Diff of the two buildlogs: -- --- b1/build.log 2021-07-15 22:26:58.125073188 +0000 +++ b2/build.log 2021-07-15 22:41:21.860643451 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 15 10:19:11 -12 2021 -I: pbuilder-time-stamp: 1626387551 +I: Current time: Fri Jul 16 12:27:18 +14 2021 +I: pbuilder-time-stamp: 1626388038 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 [./biojava-live_1.7.1-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.9iAN6AeL/trustedkeys.kbx': General error -gpgv: Signature made Mon Jan 4 03:49:41 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.TxwHzAUB/trustedkeys.kbx': General error +gpgv: Signature made Tue Jan 5 05:49:41 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,169 @@ dpkg-source: info: applying java8_instead_of_11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/27379/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2052/tmp/hooks/D01_modify_environment starting +debug: Running on jtx1b. +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/2052/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2052/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='1938a2d02f344f819a2dcef97bcb65f7' - 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='27379' - PS1='# ' - PS2='> ' + INVOCATION_ID=6320a39e17ac4833b5975a8ede7f0942 + 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=2052 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.nkitly5kkm/pbuilderrc_5Zgz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.nkitly5kkm/b1 --logfile b1/build.log biojava-live_1.7.1-9.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.nkitly5kkm/pbuilderrc_VckS --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.nkitly5kkm/b2 --logfile b2/build.log --extrapackages usrmerge biojava-live_1.7.1-9.dsc' + SUDO_GID=114 + SUDO_UID=110 + 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 12 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/27379/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 16 12:27 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 14 23:30 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/2052/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -331,7 +365,7 @@ Get: 116 http://deb.debian.org/debian bullseye/main armhf libcommons-dbcp-java all 1.4-7 [157 kB] Get: 117 http://deb.debian.org/debian bullseye/main armhf libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 118 http://deb.debian.org/debian bullseye/main armhf libhsqldb-java all 2.5.1-1 [1556 kB] -Fetched 278 MB in 24s (11.7 MB/s) +Fetched 278 MB in 25s (11.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -804,135 +838,135 @@ Setting up libgl1:armhf (1.3.2-1) ... 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:DigiCert_Global_Root_G2.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:UCA_Global_G2_Root.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:COMODO_Certification_Authority.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:emSign_Root_CA_-_C1.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:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:TWCA_Root_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:GlobalSign_ECC_Root_CA_-_R5.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:certSIGN_ROOT_CA.pem Adding debian:CFCA_EV_ROOT.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:Secure_Global_CA.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:GTS_Root_R2.pem +Adding debian:QuoVadis_Root_CA_2.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:Certum_Trusted_Network_CA.pem +Adding debian:GTS_Root_R3.pem Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.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: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: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:QuoVadis_Root_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.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:Baltimore_CyberTrust_Root.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:GlobalSign_Root_CA_-_R2.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:Certigna_Root_CA.pem +Adding debian:USERTrust_ECC_Certification_Authority.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:ACCVRAIZ1.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Starfield_Class_2_CA.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:AffirmTrust_Premium.pem +Adding debian:EC-ACC.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Buypass_Class_3_Root_CA.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: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:GTS_Root_R4.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:Certum_Trusted_Network_CA_2.pem +Adding debian:Trustwave_Global_Certification_Authority.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:Go_Daddy_Class_2_CA.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R1.pem +Adding debian:SecureTrust_CA.pem +Adding debian:Hongkong_Post_Root_CA_3.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:emSign_Root_CA_-_G1.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:COMODO_RSA_Certification_Authority.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:certSIGN_Root_CA_G2.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:Certigna.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Chambers_of_Commerce_Root_-_2008.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: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:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:Amazon_Root_CA_2.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:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:Izenpe.com.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem done. Setting up default-jre-headless (2:1.11-72) ... Setting up ant (1.10.9-4) ... @@ -995,8 +1029,45 @@ 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 (339 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 ... 23587 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/biojava-live-1.7.1/ && 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 > ../biojava-live_1.7.1-9_source.changes +hostname: Name or service not known +I: Running cd /build/biojava-live-1.7.1/ && 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 > ../biojava-live_1.7.1-9_source.changes dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.7.1-9 dpkg-buildpackage: info: source distribution unstable @@ -1021,7 +1092,7 @@ clean: BUILD SUCCESSFUL -Total time: 1 second +Total time: 10 seconds debian/rules override_dh_clean make[1]: Entering directory '/build/biojava-live-1.7.1' ant clean # most probably this is not needed when using dh - leave it to be sure ... @@ -1100,7 +1171,7 @@ [jar] Building jar: /build/biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL -Total time: 59 seconds +Total time: 1 minute 59 seconds # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1124,7 +1195,7 @@ package-biojava: BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 13 seconds #ant compile-demos ant javadocs-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1369,10 +1440,10 @@ [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] Generating /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/package-summary.html... + [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_corba.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/bibobjects_java.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... - [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_corba.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... @@ -1381,7 +1452,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 1 minute 28 seconds +Total time: 2 minutes 42 seconds touch build-stamp make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_auto_test @@ -1440,202 +1511,202 @@ runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec [junit] Running org.biojava.bio.MergeAnnotationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojava.bio.dist.DistSerTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.238 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 sec [junit] Running org.biojava.bio.dist.DistributionTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.dp.DPSerializationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.193 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.program.fastq.FastqTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.184 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest - [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec + [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.282 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.program.sax.BlastTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.53 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.426 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.26 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.208 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.074 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.462 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.258 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.235 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.958 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.743 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.485 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.413 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.778 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.33 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.057 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.917 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.606 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.456 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.445 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.781 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.732 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.792 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.113 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.278 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.123 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.643 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.069 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.337 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.372 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest - [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec [junit] Running org.biojava.bio.seq.DNAToolsTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.seq.RNAToolsTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.207 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.154 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest - [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 1.248 sec + [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 1.165 sec [junit] Test org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest FAILED [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.105 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.257 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.139 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest - [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.723 sec + [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.331 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest - [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 2.235 sec + [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.378 sec [junit] Test org.biojava.bio.seq.io.SeqIOToolsTest FAILED [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.686 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.068 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.structure.MMcifTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.931 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.48 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.146 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.12 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest - [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 7.668 sec + [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 5.741 sec [junit] Test org.biojava.bio.structure.StructurePairAlignerTest FAILED [junit] Running org.biojava.bio.structure.StructureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.157 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] Running org.biojava.bio.structure.StructureToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.129 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.178 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.409 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.643 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.925 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest @@ -1643,13 +1714,13 @@ [junit] Running org.biojava.bio.symbol.GappedSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest @@ -1657,140 +1728,140 @@ [junit] Running org.biojava.bio.symbol.PointLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.SymbolListTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.265 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.8 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.symbol.TranslationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.291 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 sec [junit] Running org.biojava.directory.OBDARegistryParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.directory.RegistryConfigurationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.directory.SystemRegistryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 sec [junit] Running org.biojava.naming.ObdaUriParserTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.ontology.OntologyTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.ontology.ParseOBOFileTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.257 sec [junit] Running org.biojava.ontology.TermImplTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.ontology.TripleImplTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.ListToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.utils.SmallMapTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.automata.NfaTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.utils.process.ExternalProcessTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.utils.regex.RegexTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.utils.walker.WalkerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.EmptyRichAnnotationTest - [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.SimpleCommentTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.SimpleCrossRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.SimpleDocRefTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.SimpleNamespaceTest - [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.012 sec [junit] Test org.biojavax.SimpleNamespaceTest FAILED [junit] Running org.biojavax.SimpleNoteTest [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.SimpleRankedDocRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojavax.SimpleRichAnnotationTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.bio.SimpleBioEntryTest [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec [junit] Test org.biojavax.bio.SimpleBioEntryTest FAILED [junit] Running org.biojavax.bio.seq.CompoundRichLocationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.117 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.259 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.147 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.085 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.236 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojavax.ga.util.GAToolsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.ga.util.WeightedSetTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.ontology.SimpleComparableOntologyTest [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojavax.ontology.SimpleComparableTermTest - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec BUILD SUCCESSFUL -Total time: 1 minute 44 seconds +Total time: 1 minute 27 seconds make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_installdocs dh_installchangelogs @@ -1820,10 +1891,10 @@ dpkg-gencontrol: warning: Depends field of package libbiojava1.7-java: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-9_all.deb'. -dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-9_all.deb'. dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-9_all.deb'. +dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-9_all.deb'. dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.7.1-9_all.deb'. +dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-9_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava-live_1.7.1-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1831,12 +1902,14 @@ 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/2052/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2052/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/27379 and its subdirectories -I: Current time: Thu Jul 15 10:26:54 -12 2021 -I: pbuilder-time-stamp: 1626388014 +I: removing directory /srv/workspace/pbuilder/2052 and its subdirectories +I: Current time: Fri Jul 16 12:41:17 +14 2021 +I: pbuilder-time-stamp: 1626388877