Diff of the two buildlogs: -- --- b1/build.log 2023-04-18 22:04:18.804789197 +0000 +++ b2/build.log 2023-04-18 22:51:28.635245658 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 18 08:49:42 -12 2023 -I: pbuilder-time-stamp: 1681850982 +I: Current time: Tue May 21 18:27:23 +14 2024 +I: pbuilder-time-stamp: 1716265643 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: copying [./biojava5-live_5.4.0+dfsg.orig.tar.gz] I: copying [./biojava5-live_5.4.0+dfsg-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 20 10:31:17 2022 -12 +gpgv: Signature made Wed Dec 21 12:31:17 2022 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava5-live_5.4.0+dfsg-5.dsc: no acceptable signature found @@ -45,135 +45,167 @@ dpkg-source: info: applying fix_ambiguous_method_call.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/138935/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 21 18:27 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='45974948f8544fb8a511f4bc7b2150cb' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='138935' - PS1='# ' - PS2='> ' + INVOCATION_ID=1e6444354cd84d688ad7e73be629a73e + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2069775 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jNShoKcE/pbuilderrc_cDZX --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jNShoKcE/b1 --logfile b1/build.log biojava5-live_5.4.0+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.jNShoKcE/pbuilderrc_XqhV --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.jNShoKcE/b2 --logfile b2/build.log --extrapackages usrmerge biojava5-live_5.4.0+dfsg-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/138935/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 21 18:27 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -664,7 +696,7 @@ Get: 395 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB] Get: 396 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB] Get: 397 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.2 [108 kB] -Fetched 501 MB in 15s (32.8 MB/s) +Fetched 501 MB in 8s (60.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -2454,8 +2486,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/biojava5-live-5.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava5-live_5.4.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/biojava5-live-5.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava5-live_5.4.0+dfsg-5_source.changes dpkg-buildpackage: info: source package biojava5-live dpkg-buildpackage: info: source version 5.4.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -2471,7 +2514,7 @@ jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf target rm -rf biojava-*/target @@ -2487,7 +2530,7 @@ dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' # Creating the directories for forester and jcolorbrewer, with symlinks. mkdir -p biojava-forester/src/main/java/ cp -a forester/org biojava-forester/src/main/java/ @@ -2502,7 +2545,7 @@ jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' # Insert the correct JSON_SIMPLE_PACKAGE in the code. find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ @@ -12712,25 +12755,25 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [02:52 min] -[INFO] biojava-core ....................................... SUCCESS [01:08 min] -[INFO] biojava-forester ................................... SUCCESS [01:46 min] -[INFO] biojava-alignment .................................. SUCCESS [ 31.610 s] -[INFO] biojava-structure .................................. SUCCESS [02:09 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 14.808 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 48.458 s] -[INFO] biojava-genome ..................................... SUCCESS [ 47.449 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 26.756 s] -[INFO] biojava-ws ......................................... SUCCESS [ 17.605 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 16.491 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 53.088 s] -[INFO] biojava-survival ................................... SUCCESS [ 22.655 s] -[INFO] biojava-ontology ................................... SUCCESS [ 21.339 s] +[INFO] biojava ............................................ SUCCESS [ 38.761 s] +[INFO] biojava-core ....................................... SUCCESS [ 18.394 s] +[INFO] biojava-forester ................................... SUCCESS [ 17.934 s] +[INFO] biojava-alignment .................................. SUCCESS [ 7.448 s] +[INFO] biojava-structure .................................. SUCCESS [ 22.781 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 2.807 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 8.082 s] +[INFO] biojava-genome ..................................... SUCCESS [ 5.076 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 4.283 s] +[INFO] biojava-ws ......................................... SUCCESS [ 3.042 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 3.407 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 10.806 s] +[INFO] biojava-survival ................................... SUCCESS [ 3.952 s] +[INFO] biojava-ontology ................................... SUCCESS [ 4.116 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 13:02 min -[INFO] Finished at: 2023-04-18T09:10:31-12:00 +[INFO] Total time: 02:32 min +[INFO] Finished at: 2024-05-21T18:34:37+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/biojava5-live-5.4.0+dfsg' dh_auto_test @@ -12792,27 +12835,27 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.788 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.173 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [INFO] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.732 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.149 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest [INFO] Running org.biojava.nbio.core.alignment.SimpleProfileTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.713 s - in org.biojava.nbio.core.alignment.SimpleProfileTest +[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.199 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [INFO] Running org.biojava.nbio.core.TestAmbiguityCompoundSet SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.655 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.134 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [INFO] Running org.biojava.nbio.core.fasta.TestFASTAReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.887 s - in org.biojava.nbio.core.fasta.TestFASTAReader +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 s - in org.biojava.nbio.core.fasta.TestFASTAReader [INFO] Running org.biojava.nbio.core.search.io.HspTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -12820,19 +12863,19 @@ getAlignment hashCode equals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.625 s - in org.biojava.nbio.core.search.io.HspTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 s - in org.biojava.nbio.core.search.io.HspTest [INFO] Running org.biojava.nbio.core.search.io.SearchIOTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.824 s - in org.biojava.nbio.core.search.io.SearchIOTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.146 s - in org.biojava.nbio.core.search.io.SearchIOTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastXMLParserTest getFileExtensions SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. setFile -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.533 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.12 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest [INFO] Running org.biojava.nbio.core.search.io.blast.BlastTabularParserTest createObjects SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". @@ -12840,126 +12883,126 @@ SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. getFileExtensions setFile -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.2 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.288 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [INFO] Running org.biojava.nbio.core.sequence.JoiningSequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.TestSequenceEquals SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.411 s - in org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.core.sequence.TestSequenceEquals [INFO] Running org.biojava.nbio.core.sequence.DNATest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.306 s - in org.biojava.nbio.core.sequence.DNATest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 s - in org.biojava.nbio.core.sequence.DNATest [INFO] Running org.biojava.nbio.core.sequence.SequenceViewTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.419 s - in org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 s - in org.biojava.nbio.core.sequence.SequenceViewTest [INFO] Running org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.497 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [INFO] Running org.biojava.nbio.core.sequence.views.WindowViewTests SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.43 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.4 s - in org.biojava.nbio.core.sequence.views.WindowViewTests [INFO] Running org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.419 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [INFO] Running org.biojava.nbio.core.sequence.TranslationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.66 s - in org.biojava.nbio.core.sequence.TranslationTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.088 s - in org.biojava.nbio.core.sequence.TranslationTest [INFO] Running org.biojava.nbio.core.sequence.location.InsdcParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.654 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.465 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.593 s - in org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.biojava.nbio.core.sequence.location.LocationTest [INFO] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.537 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.509 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.343 s - in org.biojava.nbio.core.sequence.location.LocationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.303 s - in org.biojava.nbio.core.sequence.location.LocationParserTest [INFO] Running org.biojava.nbio.core.sequence.EditSequenceTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.428 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 s - in org.biojava.nbio.core.sequence.EditSequenceTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.845 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.752 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.467 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.ABITracerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.334 s - in org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.177 s - in org.biojava.nbio.core.sequence.io.ABITracerTest [INFO] Running org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.575 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.415 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankCookbookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.629 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.788 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest [INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.407 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.165 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.455 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [INFO] Running org.biojava.nbio.core.sequence.io.GenbankWriterTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.932 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.792 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest [INFO] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.821 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.243 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest [INFO] Running org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.756 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.515 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest [INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.472 s - in org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.core.util.TestUncompressInputStream [INFO] [INFO] Results: [INFO] @@ -13010,86 +13053,86 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.476 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.15 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [INFO] Running org.biojava.nbio.phylo.TestForesterWrapper SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.487 s - in org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.173 s - in org.biojava.nbio.phylo.TestForesterWrapper [INFO] Running org.biojava.nbio.alignment.NeedlemanWunschTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.431 s - in org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.615 s - in org.biojava.nbio.alignment.NeedlemanWunschTest [INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.661 s - in org.biojava.nbio.alignment.TestSubOptimalMSA +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.236 s - in org.biojava.nbio.alignment.TestSubOptimalMSA [INFO] Running org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.828 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.179 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading [INFO] Running org.biojava.nbio.alignment.LocalAlignmentTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.552 s - in org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.128 s - in org.biojava.nbio.alignment.LocalAlignmentTest [INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest [INFO] Running org.biojava.nbio.alignment.SimpleProfilePairTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.734 s - in org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.132 s - in org.biojava.nbio.alignment.SimpleProfilePairTest [INFO] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.752 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.514 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest [INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.448 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.76 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.42 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest [INFO] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.708 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest [INFO] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.724 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.435 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [INFO] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.865 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.708 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [INFO] Running org.biojava.nbio.alignment.io.TestStockholmParser SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.52 s - in org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.352 s - in org.biojava.nbio.alignment.io.TestStockholmParser [INFO] Running org.biojava.nbio.alignment.GuideTreeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.74 s - in org.biojava.nbio.alignment.GuideTreeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.673 s - in org.biojava.nbio.alignment.GuideTreeTest [INFO] Running org.biojava.nbio.alignment.SmithWatermanTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.524 s - in org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.682 s - in org.biojava.nbio.alignment.SmithWatermanTest [INFO] Running org.biojava.nbio.alignment.TestDNAAlignment SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.645 s - in org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.284 s - in org.biojava.nbio.alignment.TestDNAAlignment [INFO] [INFO] Results: [INFO] @@ -13126,69 +13169,69 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.564 s - in org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.biojava.nbio.structure.TestVeryLongFileName [INFO] Running org.biojava.nbio.structure.TestAtomIterator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.342 s - in org.biojava.nbio.structure.TestAtomIterator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.4 s - in org.biojava.nbio.structure.TestAtomIterator [INFO] Running org.biojava.nbio.structure.ChemCompTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.002 s - in org.biojava.nbio.structure.ChemCompTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.692 s - in org.biojava.nbio.structure.ChemCompTest [INFO] Running org.biojava.nbio.structure.TestParsingCalcium -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.299 s - in org.biojava.nbio.structure.TestParsingCalcium +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.272 s - in org.biojava.nbio.structure.TestParsingCalcium [INFO] Running org.biojava.nbio.structure.Test4hhb SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.627 s - in org.biojava.nbio.structure.Test4hhb +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.58 s - in org.biojava.nbio.structure.Test4hhb [INFO] Running org.biojava.nbio.structure.AtomPositionMapTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.352 s - in org.biojava.nbio.structure.AtomPositionMapTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.184 s - in org.biojava.nbio.structure.AtomPositionMapTest [INFO] Running org.biojava.nbio.structure.Test2JA5 -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.332 s - in org.biojava.nbio.structure.Test2JA5 +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.284 s - in org.biojava.nbio.structure.Test2JA5 [INFO] Running org.biojava.nbio.structure.PdbFileFormat30Test SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.748 s - in org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.952 s - in org.biojava.nbio.structure.PdbFileFormat30Test [INFO] Running org.biojava.nbio.structure.TestAltLocs SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.9 s - in org.biojava.nbio.structure.TestAltLocs +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.461 s - in org.biojava.nbio.structure.TestAltLocs [INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.328 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.276 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier [INFO] Running org.biojava.nbio.structure.TestDownloadChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.996 s - in org.biojava.nbio.structure.TestDownloadChemCompProvider +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.519 s - in org.biojava.nbio.structure.TestDownloadChemCompProvider [INFO] Running org.biojava.nbio.structure.ElementTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.287 s - in org.biojava.nbio.structure.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 s - in org.biojava.nbio.structure.ElementTest [INFO] Running org.biojava.nbio.structure.TestAtomCache SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.98 s - in org.biojava.nbio.structure.TestAtomCache +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.25 s - in org.biojava.nbio.structure.TestAtomCache [INFO] Running org.biojava.nbio.structure.ResidueNumberTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.796 s - in org.biojava.nbio.structure.ResidueNumberTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.structure.ResidueNumberTest [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.456 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.088 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters [INFO] Running org.biojava.nbio.structure.TestURLIdentifier SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.923 s - in org.biojava.nbio.structure.TestURLIdentifier +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.751 s - in org.biojava.nbio.structure.TestURLIdentifier [INFO] Running org.biojava.nbio.structure.TestDNAAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.673 s - in org.biojava.nbio.structure.TestDNAAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.072 s - in org.biojava.nbio.structure.TestDNAAlignment [INFO] Running org.biojava.nbio.structure.TestStructureImpl SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.911 s - in org.biojava.nbio.structure.TestStructureImpl +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 s - in org.biojava.nbio.structure.TestStructureImpl [INFO] Running org.biojava.nbio.structure.validation.TestValidationReportParsing -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 12.444 s - in org.biojava.nbio.structure.validation.TestValidationReportParsing +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.223 s - in org.biojava.nbio.structure.validation.TestValidationReportParsing [INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.616 s - in org.biojava.nbio.structure.TestStructureCrossReferences +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.103 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] Running org.biojava.nbio.structure.contact.TestInterfaceFinder SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -13199,296 +13242,296 @@ - 5.477225575051661 Interface - 5.477225575051661 -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.189 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder [INFO] Running org.biojava.nbio.structure.contact.TestContactCalc -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.676 s - in org.biojava.nbio.structure.contact.TestContactCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.086 s - in org.biojava.nbio.structure.contact.TestContactCalc [INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.507 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.11 s - in org.biojava.nbio.structure.TestExperimentalTechniques [INFO] Running org.biojava.nbio.structure.TestCloning -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.256 s - in org.biojava.nbio.structure.TestCloning +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.086 s - in org.biojava.nbio.structure.TestCloning [INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.603 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.076 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign [INFO] Running org.biojava.nbio.structure.TestEntityResIndexMapping SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 4.703 s - in org.biojava.nbio.structure.TestEntityResIndexMapping +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.813 s - in org.biojava.nbio.structure.TestEntityResIndexMapping [INFO] Running org.biojava.nbio.structure.TestStructureSerialization SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.113 s - in org.biojava.nbio.structure.TestStructureSerialization +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.147 s - in org.biojava.nbio.structure.TestStructureSerialization [INFO] Running org.biojava.nbio.structure.TestEntityHeuristics SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.977 s - in org.biojava.nbio.structure.TestEntityHeuristics +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.777 s - in org.biojava.nbio.structure.TestEntityHeuristics [INFO] Running org.biojava.nbio.structure.TestBond -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.776 s - in org.biojava.nbio.structure.TestBond +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.115 s - in org.biojava.nbio.structure.TestBond [INFO] Running org.biojava.nbio.structure.TestChargeAdder -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 9.652 s - in org.biojava.nbio.structure.TestChargeAdder +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.094 s - in org.biojava.nbio.structure.TestChargeAdder [INFO] Running org.biojava.nbio.structure.HetatomImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.008 s - in org.biojava.nbio.structure.HetatomImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.213 s - in org.biojava.nbio.structure.HetatomImplTest [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.703 s - in org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Running org.biojava.nbio.structure.xtal.TestInterfaceClustering SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 15.42 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 5.288 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.364 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.082 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo [INFO] Running org.biojava.nbio.structure.xtal.TestSpaceGroup SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.121 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.169 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup [INFO] Running org.biojava.nbio.structure.TestCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.59 s - in org.biojava.nbio.structure.TestCalc +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.structure.TestCalc [INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.28 s - in org.biojava.nbio.structure.TestLoadStructureFromURL +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.093 s - in org.biojava.nbio.structure.TestLoadStructureFromURL [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPosition SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.861 s - in org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.266 s - in org.biojava.nbio.structure.geometry.TestSuperPosition [INFO] Running org.biojava.nbio.structure.geometry.TestSuperPositionQCP SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP [INFO] Running org.biojava.nbio.structure.geometry.TestUnitQuaternions -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.436 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.132 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions [INFO] Running org.biojava.nbio.structure.ResidueRangeTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.642 s - in org.biojava.nbio.structure.ResidueRangeTest +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.363 s - in org.biojava.nbio.structure.ResidueRangeTest [INFO] Running org.biojava.nbio.structure.SourceCompoundTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.632 s - in org.biojava.nbio.structure.SourceCompoundTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.056 s - in org.biojava.nbio.structure.SourceCompoundTest [INFO] Running org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.504 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.549 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.113 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 3.198 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.242 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.788 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.312 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.358 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.248 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [INFO] Running org.biojava.nbio.structure.SiteTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.653 s - in org.biojava.nbio.structure.SiteTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.476 s - in org.biojava.nbio.structure.SiteTest [INFO] Running org.biojava.nbio.structure.PDBStatusTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.415 s - in org.biojava.nbio.structure.PDBStatusTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.376 s - in org.biojava.nbio.structure.PDBStatusTest [INFO] Running org.biojava.nbio.structure.align.TestAlignDBSearchPairs -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.532 s - in org.biojava.nbio.structure.align.TestAlignDBSearchPairs +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.261 s - in org.biojava.nbio.structure.align.TestAlignDBSearchPairs [INFO] Running org.biojava.nbio.structure.align.ce.TestWebStartClient SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.652 s - in org.biojava.nbio.structure.align.ce.TestWebStartClient +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.528 s - in org.biojava.nbio.structure.align.ce.TestWebStartClient [INFO] Running org.biojava.nbio.structure.align.ce.CeCPMainTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.057 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.968 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest [INFO] Running org.biojava.nbio.structure.align.ce.TestSmallAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.36 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.456 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment [INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.44 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.416 s - in org.biojava.nbio.structure.align.TestAlignmentConsistency [INFO] Running org.biojava.nbio.structure.align.client.TestStructureName SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.573 s - in org.biojava.nbio.structure.align.client.TestStructureName +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.719 s - in org.biojava.nbio.structure.align.client.TestStructureName [INFO] Running org.biojava.nbio.structure.align.multiple.TestAFPChainConversion SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.688 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.36 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.428 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.452 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.616 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.794 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.328 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.5 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [INFO] Running org.biojava.nbio.structure.align.util.RotationAxisTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.nbio.structure.align.util.RotationAxisTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.744 s - in org.biojava.nbio.structure.align.util.RotationAxisTest [INFO] Running org.biojava.nbio.structure.align.util.AtomCacheTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.403 s - in org.biojava.nbio.structure.align.util.AtomCacheTest +[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.536 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [INFO] Running org.biojava.nbio.structure.asa.TestAsaCalc SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.516 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.591 s - in org.biojava.nbio.structure.asa.TestAsaCalc [INFO] Running org.biojava.nbio.structure.TestNucleotides -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.425 s - in org.biojava.nbio.structure.TestNucleotides +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.279 s - in org.biojava.nbio.structure.TestNucleotides [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.45 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.304 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitCluster SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 1.384 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.876 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster [INFO] Running org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.653 s - in org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.207 s - in org.biojava.nbio.structure.rcsb.RCSBLigandsFactoryTest [INFO] Running org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.827 s - in org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.217 s - in org.biojava.nbio.structure.rcsb.RCSBDescriptionFactoryTest [INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.396 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.109 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest [INFO] Running org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.931 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.236 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest [INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.376 s - in org.biojava.nbio.structure.io.TestParseOnAsymId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.085 s - in org.biojava.nbio.structure.io.TestParseOnAsymId [INFO] Running org.biojava.nbio.structure.io.TestHeaderOnly SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 12.852 s - in org.biojava.nbio.structure.io.TestHeaderOnly +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 2.408 s - in org.biojava.nbio.structure.io.TestHeaderOnly [INFO] Running org.biojava.nbio.structure.io.FastaAFPChainConverterTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.624 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.097 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest [INFO] Running org.biojava.nbio.structure.io.TestDifficultMmCIFFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 7.877 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.799 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles [INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.792 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.086 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing [INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.661 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.083 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.657 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.114 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures [INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.502 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.132 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [INFO] Running org.biojava.nbio.structure.io.TestMmCIFSpecialCases SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.909 s - in org.biojava.nbio.structure.io.TestMmCIFSpecialCases +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.structure.io.TestMmCIFSpecialCases [INFO] Running org.biojava.nbio.structure.io.TestMMCIFWriting SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.235 s - in org.biojava.nbio.structure.io.TestMMCIFWriting +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.677 s - in org.biojava.nbio.structure.io.TestMMCIFWriting [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.477 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.28 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands [INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.406 s - in org.biojava.nbio.structure.io.TestHardBioUnits +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.258 s - in org.biojava.nbio.structure.io.TestHardBioUnits [INFO] Running org.biojava.nbio.structure.io.TestTitleParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.59 s - in org.biojava.nbio.structure.io.TestTitleParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.152 s - in org.biojava.nbio.structure.io.TestTitleParsing [INFO] Running org.biojava.nbio.structure.io.TestDBRefParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.113 s - in org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 s - in org.biojava.nbio.structure.io.TestDBRefParsing [INFO] Running org.biojava.nbio.structure.io.TestShortLines SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.546 s - in org.biojava.nbio.structure.io.TestShortLines +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.419 s - in org.biojava.nbio.structure.io.TestShortLines [INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.297 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.356 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing [INFO] Running org.biojava.nbio.structure.io.TestNonDepositedFiles SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 13, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 13.544 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles +[WARNING] Tests run: 13, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 4.505 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles [INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 1.832 s - in org.biojava.nbio.structure.io.TestSiftsParsing +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.914 s - in org.biojava.nbio.structure.io.TestSiftsParsing [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 5.652 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.575 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.28 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.108 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [INFO] Running org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.888 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.44 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes [INFO] Running org.biojava.nbio.structure.io.mmcif.TestChemCompProvider SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Using PDB_DIR=/tmp as temporary file directory -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.87 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.548 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider [INFO] Running org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.171 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.099 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.332 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.094 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip [INFO] Running org.biojava.nbio.structure.io.mmtf.TestBondFinding -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.46 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.1 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.419 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.102 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfUtils SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.132 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.258 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.72 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.693 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 9.816 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.63 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader [INFO] Running org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.715 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.17 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest [INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.491 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.088 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser [INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.66 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.097 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc [INFO] [INFO] Results: [INFO] @@ -13536,18 +13579,18 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.544 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Running org.biojava.nbio.structure.gui.ViewerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.361 s - in org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.573 s - in org.biojava.nbio.structure.gui.StructureViewerTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.296 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 s - in org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.structure.gui.RenderStyleTest [INFO] Running org.biojava.nbio.structure.gui.TestAtomInfo SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.66 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 s - in org.biojava.nbio.structure.gui.TestAtomInfo [INFO] [INFO] Results: [INFO] @@ -13576,50 +13619,50 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.genome.TestLocation -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.582 s - in org.biojava.nbio.genome.TestLocation +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 s - in org.biojava.nbio.genome.TestLocation [INFO] Running org.biojava.nbio.genome.TestIssue355 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.536 s - in org.biojava.nbio.genome.TestIssue355 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.379 s - in org.biojava.nbio.genome.TestIssue355 [INFO] Running org.biojava.nbio.genome.FeatureListTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.548 s - in org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.384 s - in org.biojava.nbio.genome.FeatureListTest [INFO] Running org.biojava.nbio.genome.GeneFeatureHelperTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.648 s - in org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.532 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.TestChromosomeMappingTools SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.772 s - in org.biojava.nbio.genome.TestChromosomeMappingTools +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.nbio.genome.TestChromosomeMappingTools [INFO] Running org.biojava.nbio.genome.TestGenomeMapping -[WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 9, Time elapsed: 0.774 s - in org.biojava.nbio.genome.TestGenomeMapping +[WARNING] Tests run: 9, Failures: 0, Errors: 0, Skipped: 9, Time elapsed: 0.163 s - in org.biojava.nbio.genome.TestGenomeMapping [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.699 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.414 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.896 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.547 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.341 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.355 s - in org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.408 s - in org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.616 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.509 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.198 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.64 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.674 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.58 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.714 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.912 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.114 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqToolsTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.186 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.genome.io.fastq.FastqTest [INFO] [INFO] Results: [INFO] @@ -13648,19 +13691,19 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.protmod.phosphosite.TestAcetylation -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.579 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.101 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.508 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.895 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] Running org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 2.599 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.696 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest [INFO] Running org.biojava.nbio.protmod.structure.ProteinModificationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.489 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.107 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest [INFO] [INFO] Results: [INFO] @@ -13689,7 +13732,7 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.556 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.14 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] @@ -13721,9 +13764,9 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 30.954 s - in org.biojava.nbio.ronn.JronnTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.464 s - in org.biojava.nbio.ronn.JronnTest [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.524 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.108 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] [INFO] Results: [INFO] @@ -13752,22 +13795,22 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.539 s - in org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [INFO] Running org.biojava.nbio.aaproperties.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.192 s - in org.biojava.nbio.aaproperties.CookBookTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.816 s - in org.biojava.nbio.aaproperties.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.profeat.CookBookTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.6 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest [INFO] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.591 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.7 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [INFO] Running org.biojava.nbio.aaproperties.CommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -13784,22 +13827,22 @@ SAOV_0114,0.101,0.0525,53660.5723 SAOV_0094,0.0537,0.0767,45884.0164 SAA6008_00126,0.0955,0.0414,95002.026 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.74 s - in org.biojava.nbio.aaproperties.CommandPromptTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.152 s - in org.biojava.nbio.aaproperties.CommandPromptTest [INFO] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.648 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.36 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [INFO] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.819 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.432 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest [INFO] Running org.biojava.nbio.aaproperties.xml.ElementTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.256 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.928 s - in org.biojava.nbio.aaproperties.xml.ElementTest [INFO] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -13810,7 +13853,7 @@ NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 SequenceName,A,N,MolecularWeight NP_000257 133 aa linear PRI 27-MAR-2008,0.0451,0.0075,15043.5262 -[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.172 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [INFO] [INFO] Results: [INFO] @@ -13861,17 +13904,17 @@ SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.32 s - in org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.294 s - in org.biojava.nbio.ontology.TestOboFileParsing [INFO] Running org.biojava.nbio.ontology.TestParseSBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.971 s - in org.biojava.nbio.ontology.TestParseSBO +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 s - in org.biojava.nbio.ontology.TestParseSBO [INFO] Running org.biojava.nbio.ontology.TestParseOBO SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.963 s - in org.biojava.nbio.ontology.TestParseOBO +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.211 s - in org.biojava.nbio.ontology.TestParseOBO [INFO] [INFO] Results: [INFO] @@ -13880,25 +13923,25 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.005 s] -[INFO] biojava-core ....................................... SUCCESS [05:43 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.251 s] -[INFO] biojava-alignment .................................. SUCCESS [03:20 min] -[INFO] biojava-structure .................................. SUCCESS [20:01 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.878 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 50.977 s] +[INFO] biojava ............................................ SUCCESS [ 0.002 s] +[INFO] biojava-core ....................................... SUCCESS [05:40 min] +[INFO] biojava-forester ................................... SUCCESS [ 0.145 s] +[INFO] biojava-alignment .................................. SUCCESS [03:00 min] +[INFO] biojava-structure .................................. SUCCESS [17:01 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.015 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 50.112 s] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] -[INFO] biojava-modfinder .................................. SUCCESS [ 41.426 s] -[INFO] biojava-ws ......................................... SUCCESS [ 10.475 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [01:00 min] -[INFO] biojava-aa-prop .................................... SUCCESS [02:00 min] -[INFO] biojava-survival ................................... SUCCESS [ 1.900 s] -[INFO] biojava-ontology ................................... SUCCESS [ 41.571 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 40.165 s] +[INFO] biojava-ws ......................................... SUCCESS [ 10.053 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 20.075 s] +[INFO] biojava-aa-prop .................................... SUCCESS [01:30 min] +[INFO] biojava-survival ................................... SUCCESS [ 0.021 s] +[INFO] biojava-ontology ................................... SUCCESS [ 30.038 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 37:38 min -[INFO] Finished at: 2023-04-18T09:48:23-12:00 +[INFO] Total time: 32:43 min +[INFO] Finished at: 2024-05-21T19:07:22+14:00 [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -14102,25 +14145,25 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 5.4.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 4.929 s] -[INFO] biojava-core ....................................... SUCCESS [ 5.146 s] -[INFO] biojava-forester ................................... SUCCESS [ 1.572 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.352 s] -[INFO] biojava-structure .................................. SUCCESS [ 1.354 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.002 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 5.600 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.488 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.351 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.253 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.320 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.307 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.309 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.259 s] +[INFO] biojava ............................................ SUCCESS [ 0.661 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.070 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.051 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.042 s] +[INFO] biojava-structure .................................. SUCCESS [ 0.054 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.036 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.041 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.043 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.038 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.037 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.035 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.064 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.052 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.032 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 24.337 s -[INFO] Finished at: 2023-04-18T09:49:28-12:00 +[INFO] Total time: 1.649 s +[INFO] Finished at: 2024-05-21T19:07:25+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava5-java --javadoc --base-directory=/build/biojava5-live-5.4.0\+dfsg --non-explore Analysing pom.xml... @@ -14339,7 +14382,7 @@ jh_installjavadoc debian/rules override_dh_installdocs make[1]: Entering directory '/build/biojava5-live-5.4.0+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' dh_installdocs # Deleting calls to urchinTracker to enhance privacy. for F in $(find . -name "*.html"); do \ @@ -14377,12 +14420,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2069775/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2069775/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/138935 and its subdirectories -I: Current time: Tue Apr 18 10:04:17 -12 2023 -I: pbuilder-time-stamp: 1681855457 +I: removing directory /srv/workspace/pbuilder/2069775 and its subdirectories +I: Current time: Tue May 21 19:14:30 +14 2024 +I: pbuilder-time-stamp: 1716268470