Diff of the two buildlogs: -- --- b1/build.log 2020-07-20 05:11:45.300895822 +0000 +++ b2/build.log 2020-07-20 05:33:42.570445182 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 21 23:32:04 -12 2021 -I: pbuilder-time-stamp: 1629631924 +I: Current time: Mon Jul 20 19:11:54 +14 2020 +I: pbuilder-time-stamp: 1595221914 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 18 07:48:29 2019 -12 +gpgv: Signature made Sat Jan 19 09:48:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-2.dsc @@ -36,138 +36,172 @@ dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/61522/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/31220/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build12-i386. +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/31220/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/31220/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='0ac6d1b28f734842a887d4390a220fa4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='61522' - PS1='# ' - PS2='> ' + INVOCATION_ID=b06360dd28694649a43647b252ad2a6d + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=31220 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.ueqfUSB33L/pbuilderrc_UBAR --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/pbuilderrc_xvjR --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ueqfUSB33L/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux profitbricks-build16-i386 4.19.0-9-amd64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 21 02:47 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/61522/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 20 19:15 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 19 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/31220/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -504,7 +538,7 @@ Get: 241 http://deb.debian.org/debian buster/main i386 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 242 http://deb.debian.org/debian buster/main i386 libxmlunit-java all 1.6-1 [95.5 kB] Get: 243 http://deb.debian.org/debian buster/main i386 rdfind i386 1.4.1-1 [43.0 kB] -Fetched 412 MB in 7s (59.8 MB/s) +Fetched 412 MB in 56s (7375 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) @@ -1515,134 +1549,134 @@ Setting up ant (1.10.5-2) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:SecureSign_RootCA11.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:SecureTrust_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:thawte_Primary_Root_CA_-_G3.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:DST_Root_CA_X3.pem Adding debian:Certplus_Class_2_Primary_CA.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:GeoTrust_Universal_CA_2.pem +Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Certigna.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem +Adding debian:GeoTrust_Global_CA.pem +Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Secure_Global_CA.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:EC-ACC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:Certigna.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:thawte_Primary_Root_CA.pem -Adding debian:AffirmTrust_Premium.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:GeoTrust_Primary_Certification_Authority.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Deutsche_Telekom_Root_CA_2.pem +Adding debian:Taiwan_GRCA.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:AddTrust_External_Root.pem +Adding debian:Izenpe.com.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:GeoTrust_Universal_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem -Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:EC-ACC.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:Security_Communication_RootCA2.pem Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem -Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem -Adding debian:Taiwan_GRCA.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:GeoTrust_Universal_CA_2.pem -Adding debian:Starfield_Class_2_CA.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem -Adding debian:SecureTrust_CA.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:Certinomis_-_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem -Adding debian:GeoTrust_Global_CA.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:AddTrust_External_Root.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:Amazon_Root_CA_1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem -Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:thawte_Primary_Root_CA_-_G3.pem +Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:Izenpe.com.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:Deutsche_Telekom_Root_CA_2.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:AffirmTrust_Commercial.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:EE_Certification_Centre_Root_CA.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:GeoTrust_Universal_CA.pem -Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:LuxTrust_Global_Root_2.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:Certinomis_-_Root_CA.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:GeoTrust_Primary_Certification_Authority.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:COMODO_ECC_Certification_Authority.pem done. Setting up junit4 (4.12-8) ... Setting up liblwp-protocol-https-perl (6.07-2) ... @@ -1677,7 +1711,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1688,7 +1722,7 @@ dh clean --with javahelper jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten dh_clean rm -rf build rm -rf dist @@ -1699,13 +1733,13 @@ rm -rf doc find . -name "*.class" -delete rm -rf buildtest -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen debian/rules build dh build --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml @@ -1723,10 +1757,10 @@ sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten cd biojava-jcolorbrewer && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-jcolorbrewer/build.xml @@ -1743,7 +1777,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 12 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1759,7 +1793,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 54 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1777,7 +1811,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 2 seconds +Total time: 22 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1791,7 +1825,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 13 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1807,7 +1841,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 13 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1825,7 +1859,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 8 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1841,7 +1875,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 10 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1856,7 +1890,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 5 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1874,7 +1908,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 26 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1892,7 +1926,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 2 seconds +Total time: 23 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1908,7 +1942,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 16 seconds cd biojava-ontology && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1926,7 +1960,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 21 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1942,7 +1976,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 10 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1956,7 +1990,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 9 seconds cd biojava-ws && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1972,7 +2006,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 1 second +Total time: 16 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1986,7 +2020,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 2 seconds +Total time: 15 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2278,11 +2312,11 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 12 seconds +Total time: 1 minute 28 seconds # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -2311,169 +2345,169 @@ [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.327 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.327 sec [junit] - [junit] Testcase: testGetIndexOf took 0.018 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0 sec + [junit] Testcase: testGetIndexOf took 0.095 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetNumGaps took 0 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0 sec - [junit] Testcase: testGetSequenceIndexAt took 0.001 sec - [junit] Testcase: testGetAccession took 0 sec - [junit] Testcase: testToString took 0.001 sec + [junit] Testcase: testGetSequenceIndexAt took 0 sec + [junit] Testcase: testGetAccession took 0.001 sec + [junit] Testcase: testToString took 0.006 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec [junit] Testcase: testCountCompounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAt took 0 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.002 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.001 sec + [junit] Testcase: testGetAsList took 0.011 sec [junit] Testcase: testGetOriginalSequence took 0.001 sec - [junit] Testcase: testGetCompoundAt took 0 sec + [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testGetLength took 0 sec [junit] Testcase: testIsCircular took 0 sec - [junit] Testcase: testGetEnd took 0.001 sec - [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec + [junit] Testcase: testGetEnd took 0 sec + [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec [junit] Testcase: testGetOverlapCount took 0 sec - [junit] Testcase: testGetCompoundSet took 0 sec - [junit] Testcase: testGetLocationInAlignment took 0.001 sec - [junit] Testcase: testIterator took 0 sec - [junit] Testcase: testGetSequenceAsString took 0 sec + [junit] Testcase: testGetCompoundSet took 0.001 sec + [junit] Testcase: testGetLocationInAlignment took 0.002 sec + [junit] Testcase: testIterator took 0.001 sec + [junit] Testcase: testGetSequenceAsString took 0.001 sec [junit] Testcase: testGetLastIndexOf took 0 sec - [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.001 sec + [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.096 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.096 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.366 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.366 sec [junit] - [junit] Testcase: testGetIndexOf took 0.033 sec + [junit] Testcase: testGetIndexOf took 0.158 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec - [junit] Testcase: testToStringInt took 0.005 sec - [junit] Testcase: testToString took 0.001 sec - [junit] Testcase: testToStringFormatted took 0.009 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.002 sec + [junit] Testcase: testToStringInt took 0.012 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testToStringFormatted took 0.033 sec [junit] Testcase: testSimpleProfile took 0 sec [junit] Testcase: testGetSize took 0 sec [junit] Testcase: testGetAlignedSequenceS took 0 sec - [junit] Testcase: testGetAlignedSequences took 0 sec - [junit] Testcase: testGetOriginalSequences took 0 sec + [junit] Testcase: testGetAlignedSequences took 0.001 sec + [junit] Testcase: testGetOriginalSequences took 0.005 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0 sec [junit] Testcase: testGetAlignedSequencesSArray took 0 sec [junit] Testcase: testGetIndicesAt took 0.002 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignedSequencesIntArray took 0.001 sec [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec [junit] Testcase: testGetLength took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec - [junit] Testcase: testGetCompoundSet took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundSet took 0.001 sec [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec [junit] Testcase: testIterator took 0.001 sec - [junit] Testcase: testGetLastIndexOf took 0 sec + [junit] Testcase: testGetLastIndexOf took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.82 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.82 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.032 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.612 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetQuery took 0.019 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 sec [junit] Testcase: testGetIndexInTargetAt took 0 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.008 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec - [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInQueryAt took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec - [junit] Testcase: testGetNumIdenticals took 0.001 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetNumIdenticals took 0.002 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec - [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryAt took 0 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInTargetAt took 0 sec + [junit] Testcase: testGetIndexInQueryAt took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec - [junit] Testcase: testGetNumSimilars took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetNumSimilars took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.151 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.151 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.027 sec + [junit] Testcase: testGetAlignment took 1.386 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 5.842 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 5.842 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml - [junit] Aug 21, 2021 11:34:00 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Jul 20, 2020 7:28:17 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Aug 21, 2021 11:34:00 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Jul 20, 2020 7:28:17 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testConstructorWithEvalueHspFilter took 0.092 sec + [junit] Testcase: testConstructorWithEvalueHspFilter took 4.206 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2484,8 +2518,8 @@ [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] - [junit] Testcase: testConstructorWithFactoryGuess took 0.052 sec - [junit] Testcase: testConstructorWithoutFactoryGuess took 0.002 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.919 sec + [junit] Testcase: testConstructorWithoutFactoryGuess took 0.01 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2500,7 +2534,7 @@ BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed -Total time: 3 seconds +Total time: 46 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -2515,32 +2549,32 @@ [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.709 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.709 sec [junit] - [junit] Testcase: testGetQuery took 0.027 sec - [junit] Testcase: testGetScore took 0.011 sec - [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec - [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testGetQuery took 0.45 sec + [junit] Testcase: testGetScore took 0.065 sec + [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testGetMinScore took 0.001 sec [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec - [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.745 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.745 sec [junit] - [junit] Testcase: testGetQuery took 0.028 sec - [junit] Testcase: testGetScore took 0.011 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0 sec - [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec + [junit] Testcase: testGetQuery took 0.18 sec + [junit] Testcase: testGetScore took 0.127 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.001 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.063 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.063 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -2552,157 +2586,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.061 sec - [junit] Testcase: testToString took 0.002 sec - [junit] Testcase: testGetScoreMatrix took 0.002 sec - [junit] Testcase: testGetRoot took 0.014 sec - [junit] Testcase: testGetSequences took 0.001 sec - [junit] Testcase: testGetDistanceMatrix took 0.001 sec - [junit] Testcase: testGetAllPairsScores took 0.001 sec - [junit] Testcase: testIterator took 0.001 sec + [junit] Testcase: testGuideTree took 1.589 sec + [junit] Testcase: testToString took 0.005 sec + [junit] Testcase: testGetScoreMatrix took 0.01 sec + [junit] Testcase: testGetRoot took 0.289 sec + [junit] Testcase: testGetSequences took 0.007 sec + [junit] Testcase: testGetDistanceMatrix took 0.002 sec + [junit] Testcase: testGetAllPairsScores took 0.003 sec + [junit] Testcase: testIterator took 0.004 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.659 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.659 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.046 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.533 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.205 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.953 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.953 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.028 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.696 sec [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.011 sec - [junit] Testcase: should_align_middle_anchor took 0.01 sec + [junit] Testcase: testGetComputationTime took 0.215 sec + [junit] Testcase: should_align_middle_anchor took 0.042 sec [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetScore took 0 sec - [junit] Testcase: testNeedlemanWunsch took 0 sec - [junit] Testcase: should_align_all_anchored took 0 sec - [junit] Testcase: testGetScoreMatrix took 0 sec - [junit] Testcase: testGetPair took 0.001 sec - [junit] Testcase: should_align_multiple_anchors took 0 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.002 sec - [junit] Testcase: testGetProfile took 0 sec - [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: should_align_ending_anchor took 0 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec - [junit] Testcase: testComplex took 0.004 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.007 sec - [junit] Testcase: should_align_starting_anchor took 0.001 sec + [junit] Testcase: testGetScore took 0.004 sec + [junit] Testcase: testNeedlemanWunsch took 0.001 sec + [junit] Testcase: should_align_all_anchored took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: should_align_multiple_anchors took 0.002 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.006 sec + [junit] Testcase: testGetProfile took 0.002 sec + [junit] Testcase: testGetMinScore took 0.002 sec + [junit] Testcase: should_align_ending_anchor took 0.001 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec + [junit] Testcase: testComplex took 0.031 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.021 sec + [junit] Testcase: should_align_starting_anchor took 0.066 sec [junit] Testcase: anchors_should_not_change_score took 0 sec - [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetMaxScore took 0 sec - [junit] Testcase: testIntOverflowBug took 0.117 sec + [junit] Testcase: testIntOverflowBug took 0.485 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 sec [junit] - [junit] Testcase: testOpenPenalty took 0.002 sec + [junit] Testcase: testOpenPenalty took 0.004 sec [junit] Testcase: testType took 0 sec [junit] Testcase: testExtensionPenalty took 0 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec - [junit] Testcase: testSimpleGapPenalty took 0 sec + [junit] Testcase: testSimpleGapPenalty took 0.001 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 sec [junit] - [junit] Testcase: testGetQuery took 0.042 sec + [junit] Testcase: testGetQuery took 0.409 sec [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testSimpleProfilePair took 0.002 sec + [junit] Testcase: testSimpleProfilePair took 0.031 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.282 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.282 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.04 sec - [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.001 sec - [junit] Testcase: testGetQuery took 0.001 sec - [junit] Testcase: testGetScore took 0.001 sec - [junit] Testcase: testGetScoreMatrix took 0.002 sec - [junit] Testcase: testGetPair took 0.003 sec - [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: testIsStoringScoreMatrix took 0 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.011 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0 sec - [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.912 sec + [junit] Testcase: testGetGapPenalty took 0.003 sec + [junit] Testcase: testGetComputationTime took 0.003 sec + [junit] Testcase: testGetQuery took 0.004 sec + [junit] Testcase: testGetScore took 0.019 sec + [junit] Testcase: testGetScoreMatrix took 0.019 sec + [junit] Testcase: testGetPair took 0.017 sec + [junit] Testcase: testGetProfile took 0.004 sec + [junit] Testcase: testGetMinScore took 0.014 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.042 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.001 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.002 sec + [junit] Testcase: testGetTarget took 0.008 sec + [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.567 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.003 sec - [junit] Testcase: testSetDescription took 0.01 sec - [junit] Testcase: testToString took 0.015 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.061 sec + [junit] Testcase: testSetDescription took 0.176 sec + [junit] Testcase: testToString took 0.123 sec [junit] Testcase: testCaseEquivalence took 0.001 sec - [junit] Testcase: test took 0.005 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.004 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.001 sec - [junit] Testcase: testSetName took 0.002 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.001 sec + [junit] Testcase: test took 0.023 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.019 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.004 sec + [junit] Testcase: testSetName took 0.005 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.004 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.027 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.655 sec [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.011 sec + [junit] Testcase: testGetComputationTime took 0.13 sec [junit] Testcase: testGetQuery took 0 sec - [junit] Testcase: testGetScore took 0 sec + [junit] Testcase: testGetScore took 0.023 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec - [junit] Testcase: testGetPair took 0.002 sec - [junit] Testcase: testSmithWaterman took 0.001 sec - [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testGetPair took 0.01 sec + [junit] Testcase: testSmithWaterman took 0.004 sec + [junit] Testcase: testGetProfile took 0.002 sec + [junit] Testcase: testGetMinScore took 0.005 sec [junit] Testcase: testIsStoringScoreMatrix took 0 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.014 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.058 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.001 sec - [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.001 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.004 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.003 sec [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec - [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec + [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0.001 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.739 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.739 sec [junit] - [junit] Testcase: testGetComputationTime took 0.038 sec - [junit] Testcase: testGuanUberbacher took 0.001 sec - [junit] Testcase: testGetScore took 0 sec - [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: testGetComputationTime took 0.344 sec + [junit] Testcase: testGuanUberbacher took 0.008 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetPair took 0.005 sec [junit] Testcase: testGetProfile took 0.001 sec - [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: should_align_shorter_target took 0.009 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: should_align_shorter_target took 0.138 sec [junit] Testcase: should_align_multiple_cuts took 0.001 sec [junit] Testcase: testGetMaxScore took 0 sec - [junit] Testcase: should_align_shorter_query took 0 sec + [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 1 minute 28 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -2725,8 +2759,8 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.496 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.496 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -2734,12 +2768,12 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 0.294 sec - [junit] Testcase: testExample1 took 0.014 sec - [junit] Testcase: testExample2 took 0.004 sec - [junit] Testcase: testExample3 took 0.013 sec - [junit] Testcase: testExample1WithCSV took 0.01 sec - [junit] Testcase: testWithCases took 0.002 sec + [junit] Testcase: testAdvancedXMLExample took 6.275 sec + [junit] Testcase: testExample1 took 0.064 sec + [junit] Testcase: testExample2 took 0.01 sec + [junit] Testcase: testExample3 took 0.02 sec + [junit] Testcase: testExample1WithCSV took 0.04 sec + [junit] Testcase: testWithCases took 0.006 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2747,14 +2781,14 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.314 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.939 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.939 sec [junit] - [junit] Testcase: shortExample1 took 0.014 sec - [junit] Testcase: shortExample2 took 0.243 sec - [junit] Testcase: shortExample3 took 0.029 sec + [junit] Testcase: shortExample1 took 0.072 sec + [junit] Testcase: shortExample2 took 1.631 sec + [junit] Testcase: shortExample3 took 0.089 sec [junit] Testcase: shortExample4 took 0.001 sec - [junit] Testcase: shortExample5 took 0.002 sec + [junit] Testcase: shortExample5 took 0.005 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2762,19 +2796,19 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.37 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.37 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.564 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.564 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 0.296 sec - [junit] Testcase: testExample1 took 0.009 sec - [junit] Testcase: testExample2 took 0.005 sec - [junit] Testcase: testExample3 took 0.005 sec - [junit] Testcase: testExample1WithCSV took 0.005 sec - [junit] Testcase: testWithCases took 0.004 sec + [junit] Testcase: testAdvancedXMLExample took 3.732 sec + [junit] Testcase: testExample1 took 0.026 sec + [junit] Testcase: testExample2 took 0.02 sec + [junit] Testcase: testExample3 took 0.02 sec + [junit] Testcase: testExample1WithCSV took 0.035 sec + [junit] Testcase: testWithCases took 0.014 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] WARNING: An illegal reflective access operation has occurred @@ -2782,8 +2816,8 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.126 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.126 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. @@ -2998,39 +3032,39 @@ [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAbsorbance took 0.016 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 0.264 sec - [junit] Testcase: testEnrichment took 0.006 sec - [junit] Testcase: testApliphaticIndex took 0.001 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.003 sec + [junit] Testcase: testAbsorbance took 0.164 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 5.756 sec + [junit] Testcase: testEnrichment took 0.02 sec + [junit] Testcase: testApliphaticIndex took 0.002 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.054 sec [junit] Testcase: testApliphaticIndexNull took 0 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.001 sec - [junit] Testcase: testAbsorbanceNull took 0 sec - [junit] Testcase: testIsoelectricPointNull took 0 sec - [junit] Testcase: testAverageHydropathy took 0 sec - [junit] Testcase: testExtinctionCoefficient took 0.001 sec - [junit] Testcase: testAAComposition took 0 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.017 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.004 sec + [junit] Testcase: testAbsorbanceNull took 0.001 sec + [junit] Testcase: testIsoelectricPointNull took 0.001 sec + [junit] Testcase: testAverageHydropathy took 0.001 sec + [junit] Testcase: testExtinctionCoefficient took 0.002 sec + [junit] Testcase: testAAComposition took 0.005 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.233 sec [junit] Testcase: testMolecularWeight took 0.001 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.001 sec - [junit] Testcase: testNetChargeNull took 0.001 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec + [junit] Testcase: testNetChargeNull took 0 sec [junit] Testcase: testExtinctionCoefficientNull took 0 sec - [junit] Testcase: testNetCharge took 0.064 sec + [junit] Testcase: testNetCharge took 0.596 sec [junit] Testcase: testEnrichmentNull took 0 sec - [junit] Testcase: testInstabilityIndexNull took 0 sec + [junit] Testcase: testInstabilityIndexNull took 0.005 sec [junit] Testcase: testAverageHydropathyNull took 0 sec - [junit] Testcase: testMolecularWeightXML took 0.025 sec - [junit] Testcase: testInstabilityIndex took 0 sec + [junit] Testcase: testMolecularWeightXML took 0.199 sec + [junit] Testcase: testInstabilityIndex took 0.004 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 sec [junit] - [junit] Testcase: testFake took 0 sec + [junit] Testcase: testFake took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.295 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.295 sec [junit] [junit] Testcase: testFakeTest took 0.001 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest @@ -3040,20 +3074,20 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.447 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.447 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.348 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.348 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: generateSchema took 0.198 sec - [junit] Testcase: readWithIDXml took 0.076 sec - [junit] Testcase: readMinXml took 0.027 sec - [junit] Testcase: readAdvancedXml took 0.013 sec - [junit] Testcase: generateXml took 0.015 sec - [junit] Testcase: readXml took 0.023 sec + [junit] Testcase: generateSchema took 1.217 sec + [junit] Testcase: readWithIDXml took 0.533 sec + [junit] Testcase: readMinXml took 0.192 sec + [junit] Testcase: readAdvancedXml took 0.06 sec + [junit] Testcase: generateXml took 0.064 sec + [junit] Testcase: readXml took 0.191 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest [junit] WARNING: An illegal reflective access operation has occurred @@ -3061,21 +3095,21 @@ [junit] WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector [junit] WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations [junit] WARNING: All illegal access operations will be denied in a future release - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.343 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.51 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.51 sec [junit] - [junit] Testcase: generateSchema took 0.203 sec - [junit] Testcase: generateXml took 0.033 sec - [junit] Testcase: readXml took 0.085 sec + [junit] Testcase: generateSchema took 2.911 sec + [junit] Testcase: generateXml took 0.121 sec + [junit] Testcase: readXml took 0.346 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 sec [junit] - [junit] Testcase: testFake took 0 sec + [junit] Testcase: testFake took 0.027 sec BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 1 minute 4 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -3092,7 +3126,7 @@ [echo] Using java version 11.0.6 BUILD SUCCESSFUL -Total time: 1 second +Total time: 9 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -3108,24 +3142,24 @@ [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 sec [junit] - [junit] Testcase: testConvert took 0.061 sec + [junit] Testcase: testConvert took 0.353 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.245 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.245 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.003 sec + [junit] Testcase: testBuildAppendSequence took 0.068 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec - [junit] Testcase: testBuildDefaultVariant took 0 sec + [junit] Testcase: testBuildDefaultVariant took 0.001 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec - [junit] Testcase: testBuildNullAppendQuality took 0.001 sec + [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec @@ -3133,20 +3167,20 @@ [junit] Testcase: testBuildNullSequence took 0 sec [junit] Testcase: testBuildMissingDescription took 0 sec [junit] Testcase: testBuildNullVariant took 0 sec - [junit] Testcase: testBuildDefault took 0 sec + [junit] Testcase: testBuildDefault took 0.001 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0 sec [junit] Testcase: testBuildMultiple took 0 sec [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] - [junit] Testcase: testImmutable took 0.002 sec - [junit] Testcase: testBuilder took 0.002 sec + [junit] Testcase: testImmutable took 0.003 sec + [junit] Testcase: testBuilder took 0.015 sec [junit] Testcase: testVariant took 0 sec - [junit] Testcase: testQuality took 0.002 sec + [junit] Testcase: testQuality took 0.003 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec @@ -3154,17 +3188,17 @@ [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.002 sec + [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.008 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.031 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.066 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec - [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec + [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec [junit] Testcase: testConvertNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec @@ -3173,7 +3207,7 @@ [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec - [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec @@ -3182,10 +3216,10 @@ [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec - [junit] Testcase: testToListNotAList took 0.001 sec + [junit] Testcase: testToListNotAList took 0.066 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec - [junit] Testcase: testQualityScores took 0.003 sec + [junit] Testcase: testQualityScores took 0.045 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec @@ -3194,170 +3228,170 @@ [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testToList took 0.001 sec + [junit] Testcase: testToList took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.002 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0 sec + [junit] Testcase: testParseFastqVariant took 0.004 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec - [junit] Testcase: testIsSanger took 0.002 sec + [junit] Testcase: testIsSanger took 0.007 sec [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.338 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.732 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.732 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.021 sec - [junit] Testcase: testWrappingAsIllumina took 0.002 sec - [junit] Testcase: testValidateDescription took 0.005 sec - [junit] Testcase: testValidateRepeatDescription took 0.002 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.001 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.001 sec - [junit] Testcase: testLongReadsAsIllumina took 0.002 sec - [junit] Testcase: testParseNullReadable took 0 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.011 sec - [junit] Testcase: testParse took 0.001 sec + [junit] Testcase: testFullRangeAsIllumina took 0.128 sec + [junit] Testcase: testWrappingAsIllumina took 0.003 sec + [junit] Testcase: testValidateDescription took 0.009 sec + [junit] Testcase: testValidateRepeatDescription took 0.003 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.013 sec + [junit] Testcase: testMiscRnaAsIllumina took 0.003 sec + [junit] Testcase: testLongReadsAsIllumina took 0.013 sec + [junit] Testcase: testParseNullReadable took 0.002 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.264 sec + [junit] Testcase: testReadEmptyFile took 0.001 sec + [junit] Testcase: testErrorExamples took 0.194 sec + [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.001 sec - [junit] Testcase: testReadEmptyInputStream took 0 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0 sec - [junit] Testcase: testMultipleWrappedQuality took 0 sec + [junit] Testcase: testWrappedSequence took 0.002 sec + [junit] Testcase: testReadEmptyInputStream took 0.001 sec + [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testReadFile took 0.017 sec + [junit] Testcase: testMultipleWrappedQuality took 0.003 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0 sec + [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0 sec - [junit] Testcase: testWrappedQuality took 0 sec + [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.004 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.008 sec [junit] Testcase: testAppendVararg took 0 sec - [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec - [junit] Testcase: testWriteFileIterable took 0.01 sec + [junit] Testcase: testCreateFastq took 0 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.013 sec + [junit] Testcase: testWriteFileIterable took 0.068 sec [junit] Testcase: testWriteOutputStreamIterable took 0 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.001 sec + [junit] Testcase: testWriteFileVararg took 0.019 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.021 sec - [junit] Testcase: testFullRangeAsSanger took 0.002 sec - [junit] Testcase: testWrappingOriginal took 0.001 sec - [junit] Testcase: testLongReadsOriginal took 0.002 sec - [junit] Testcase: testMiscDnaOriginal took 0.001 sec - [junit] Testcase: testMiscRnaOriginal took 0.001 sec - [junit] Testcase: testValidateDescription took 0.004 sec - [junit] Testcase: testValidateRepeatDescription took 0.001 sec - [junit] Testcase: testFullRangeOriginal took 0.001 sec - [junit] Testcase: testWrappingAsSanger took 0.001 sec - [junit] Testcase: testLongReadsAsSanger took 0.001 sec - [junit] Testcase: testMiscDnaAsSanger took 0.001 sec + [junit] Testcase: testMiscRnaAsSanger took 0.065 sec + [junit] Testcase: testFullRangeAsSanger took 0.005 sec + [junit] Testcase: testWrappingOriginal took 0.005 sec + [junit] Testcase: testLongReadsOriginal took 0.008 sec + [junit] Testcase: testMiscDnaOriginal took 0.003 sec + [junit] Testcase: testMiscRnaOriginal took 0.003 sec + [junit] Testcase: testValidateDescription took 0.021 sec + [junit] Testcase: testValidateRepeatDescription took 0.003 sec + [junit] Testcase: testFullRangeOriginal took 0.002 sec + [junit] Testcase: testWrappingAsSanger took 0.002 sec + [junit] Testcase: testLongReadsAsSanger took 0.004 sec + [junit] Testcase: testMiscDnaAsSanger took 0.002 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.025 sec [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.009 sec - [junit] Testcase: testParse took 0.001 sec + [junit] Testcase: testErrorExamples took 0.035 sec + [junit] Testcase: testParse took 0.009 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.001 sec - [junit] Testcase: testReadEmptyInputStream took 0 sec + [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0 sec - [junit] Testcase: testMultipleWrappedQuality took 0.001 sec + [junit] Testcase: testReadFile took 0.016 sec + [junit] Testcase: testMultipleWrappedQuality took 0.132 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0 sec + [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0 sec - [junit] Testcase: testWrappedQuality took 0 sec + [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.01 sec + [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.005 sec + [junit] Testcase: testConvertNotSangerVariant took 0.072 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec - [junit] Testcase: testWriteFileIterable took 0.009 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.006 sec + [junit] Testcase: testWriteFileIterable took 0.056 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.001 sec + [junit] Testcase: testWriteFileVararg took 0.036 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.074 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.663 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.021 sec - [junit] Testcase: testFullRangeAsSolexa took 0.002 sec - [junit] Testcase: testValidateDescription took 0.005 sec - [junit] Testcase: testValidateRepeatDescription took 0.001 sec - [junit] Testcase: testWrappingAsSolexa took 0.001 sec - [junit] Testcase: testLongReadsAsSolexa took 0.002 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.001 sec - [junit] Testcase: testParseNullReadable took 0 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.011 sec - [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.01 sec - [junit] Testcase: testParse took 0.001 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.064 sec + [junit] Testcase: testFullRangeAsSolexa took 0.009 sec + [junit] Testcase: testValidateDescription took 0.011 sec + [junit] Testcase: testValidateRepeatDescription took 0.003 sec + [junit] Testcase: testWrappingAsSolexa took 0.003 sec + [junit] Testcase: testLongReadsAsSolexa took 0.006 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec + [junit] Testcase: testParseNullReadable took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.081 sec + [junit] Testcase: testReadEmptyFile took 0.009 sec + [junit] Testcase: testErrorExamples took 0.079 sec + [junit] Testcase: testParse took 0.155 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0 sec - [junit] Testcase: testReadEmptyInputStream took 0.001 sec + [junit] Testcase: testWrappedSequence took 0.002 sec + [junit] Testcase: testReadEmptyInputStream took 0.036 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0 sec - [junit] Testcase: testMultipleWrappedQuality took 0.001 sec - [junit] Testcase: testCreateFastqReader took 0 sec + [junit] Testcase: testReadFile took 0.002 sec + [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0 sec - [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0.056 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0 sec + [junit] Testcase: testWrappedQuality took 0.002 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.235 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.005 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.01 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec - [junit] Testcase: testWriteFileIterable took 0.01 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.006 sec + [junit] Testcase: testWriteFileIterable took 0.143 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec - [junit] Testcase: testCreateFastqWriter took 0.001 sec - [junit] Testcase: testWriteFileVararg took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testWriteFileVararg took 0.032 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.233 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.001 sec - [junit] Testcase: testStreamNullListener took 0.001 sec + [junit] Testcase: testStreamNullVariant took 0.012 sec + [junit] Testcase: testStreamNullListener took 0.007 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 33 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -3378,39 +3412,39 @@ [echo] Using java version 11.0.6 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [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: 0.02 sec [junit] - [junit] Testcase: testMe took 0 sec + [junit] Testcase: testMe took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] [junit] Testcase: testSomeMethod took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec [junit] - [junit] Testcase: testGetColor took 0.002 sec + [junit] Testcase: testGetColor took 0.004 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec - [junit] Testcase: testGetSelection took 0.002 sec - [junit] Testcase: testRepaint took 0.001 sec - [junit] Testcase: testSetSelection took 0 sec + [junit] Testcase: testGetSelection took 0.003 sec + [junit] Testcase: testRepaint took 0 sec + [junit] Testcase: testSetSelection took 0.001 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec - [junit] Testcase: testSetStyle took 0.001 sec + [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest - [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: 0.007 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec [junit] - [junit] Testcase: testStructureLoad took 0 sec + [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 2 seconds +Total time: 15 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -3425,8 +3459,8 @@ [echo] Using java version 11.0.6 BUILD SUCCESSFUL -Total time: 1 second -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +Total time: 9 seconds +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with javahelper @@ -3434,7 +3468,7 @@ dh_prep dh_install debian/rules override_jh_installjavadoc -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird betreten jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ /usr/share/doc/openjdk-11-jre-headless \ @@ -3455,7 +3489,7 @@ Failed moving /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-jre-headless/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-jre-headless/api/jquery/jquery-3.3.1.js Making 20 links. -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: Verzeichnis „/build/biojava4-live-4.2.12+dfsg“ wird verlassen dh_installdocs dh_installchangelogs dh_lintian @@ -3473,21 +3507,23 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-2_all.deb'. -dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb'. -dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-2_all.deb'. +dpkg-deb: Paket »libbiojava4-java« wird in »../libbiojava4-java_4.2.12+dfsg-2_all.deb« gebaut. +dpkg-deb: Paket »libbiojava4-java-doc« wird in »../libbiojava4-java-doc_4.2.12+dfsg-2_all.deb« gebaut. +dpkg-deb: Paket »libbiojava4.0-java« wird in »../libbiojava4.0-java_4.2.12+dfsg-2_all.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/31220/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/31220/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/61522 and its subdirectories -I: Current time: Sat Aug 21 23:34:42 -12 2021 -I: pbuilder-time-stamp: 1629632082 +I: removing directory /srv/workspace/pbuilder/31220 and its subdirectories +I: Current time: Mon Jul 20 19:33:42 +14 2020 +I: pbuilder-time-stamp: 1595223222