Diff of the two buildlogs: -- --- b1/build.log 2023-04-25 12:00:54.179120949 +0000 +++ b2/build.log 2023-04-25 12:56:58.949939895 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 27 05:15:47 -12 2024 -I: pbuilder-time-stamp: 1716830147 +I: Current time: Wed Apr 26 02:00:56 +14 2023 +I: pbuilder-time-stamp: 1682424056 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 [./biojava6-live_6.1.0+dfsg.orig.tar.gz] I: copying [./biojava6-live_6.1.0+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Feb 6 22:35:54 2023 -12 +gpgv: Signature made Wed Feb 8 00:35:54 2023 +14 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biojava6-live_6.1.0+dfsg-4.dsc: no acceptable signature found @@ -40,135 +40,167 @@ dpkg-source: info: applying remove_tests_needing_junitx.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/135845/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4041559/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Apr 26 02:01 /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/4041559/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4041559/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=16' - 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=15' + 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='144ee7ae4f94484cbba6e4cc712c75ae' - 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='135845' - PS1='# ' - PS2='> ' + INVOCATION_ID=b30ab7304329432388313981ba2ddc28 + 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=4041559 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.MqQJDVSU/pbuilderrc_xXpe --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.MqQJDVSU/b1 --logfile b1/build.log biojava6-live_6.1.0+dfsg-4.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://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MqQJDVSU/pbuilderrc_Y2xi --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.MqQJDVSU/b2 --logfile b2/build.log --extrapackages usrmerge biojava6-live_6.1.0+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 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 + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 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 2023 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 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 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 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 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 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 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 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 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 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 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 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 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 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 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/135845/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 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 03:20 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 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 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 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 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 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 Apr 26 02:01 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 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 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 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 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 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/4041559/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -661,7 +693,7 @@ 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 18s (28.3 MB/s) +Fetched 501 MB in 13s (39.5 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.) @@ -2451,8 +2483,19 @@ 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/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/4041559/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/4041559/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/biojava6-live-6.1.0+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 > ../biojava6-live_6.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package biojava6-live dpkg-buildpackage: info: source version 6.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -2468,7 +2511,7 @@ jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/biojava6-live-6.1.0+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 @@ -2484,7 +2527,7 @@ dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/biojava6-live-6.1.0+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/ @@ -2499,7 +2542,7 @@ jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/biojava6-live-6.1.0+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 \ @@ -12365,26 +12408,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [02:46 min] -[INFO] biojava-core ....................................... SUCCESS [01:02 min] -[INFO] biojava-forester ................................... SUCCESS [ 58.457 s] -[INFO] biojava-alignment .................................. SUCCESS [ 20.407 s] -[INFO] biojava-structure .................................. SUCCESS [01:08 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 12.152 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 32.774 s] -[INFO] biojava-genome ..................................... SUCCESS [ 20.600 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 17.550 s] -[INFO] biojava-ws ......................................... SUCCESS [ 14.670 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 14.605 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 20.309 s] -[INFO] biojava-survival ................................... SUCCESS [ 21.428 s] -[INFO] biojava-ontology ................................... SUCCESS [ 18.160 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 9.726 s] +[INFO] biojava ............................................ SUCCESS [ 55.955 s] +[INFO] biojava-core ....................................... SUCCESS [ 52.571 s] +[INFO] biojava-forester ................................... SUCCESS [ 27.266 s] +[INFO] biojava-alignment .................................. SUCCESS [ 9.802 s] +[INFO] biojava-structure .................................. SUCCESS [ 59.031 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 14.279 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 26.110 s] +[INFO] biojava-genome ..................................... SUCCESS [ 14.035 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 7.597 s] +[INFO] biojava-ws ......................................... SUCCESS [ 4.227 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 3.445 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 8.784 s] +[INFO] biojava-survival ................................... SUCCESS [ 5.630 s] +[INFO] biojava-ontology ................................... SUCCESS [ 4.358 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 2.281 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 09:24 min -[INFO] Finished at: 2024-05-27T05:32:44-12:00 +[INFO] Total time: 05:03 min +[INFO] Finished at: 2023-04-26T02:10:07+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/biojava6-live-6.1.0+dfsg' dh_auto_test @@ -12450,47 +12493,47 @@ 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: 0.403 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.218 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet [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: 0.48 s - in org.biojava.nbio.core.alignment.SimpleProfileTest +[WARNING] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.124 s - in org.biojava.nbio.core.alignment.SimpleProfileTest [INFO] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest 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: 0.34 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest +[WARNING] Tests run: 35, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.108 s - in org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest 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: 1.228 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.621 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelperTest [INFO] Running org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest 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: 1.224 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.968 s - in org.biojava.nbio.core.alignment.matrices.AAindexFactoryTest [INFO] Running org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest 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: 0.672 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.367 s - in org.biojava.nbio.core.alignment.matrices.DefaultAAIndexProviderTest [INFO] Running org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest 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: 6.124 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.133 s - in org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixTest [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: 0.244 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest +[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.core.alignment.SimpleSequencePairTest [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: 0.168 s - in org.biojava.nbio.core.fasta.TestFASTAReader +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 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 @@ -12498,19 +12541,19 @@ getAlignment hashCode equals -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.search.io.HspTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 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: 0.308 s - in org.biojava.nbio.core.search.io.SearchIOTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.212 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: 0.15 s - in org.biojava.nbio.core.search.io.blast.BlastXMLParserTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.107 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". @@ -12518,180 +12561,180 @@ 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: 4.2 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.18 s - in org.biojava.nbio.core.search.io.blast.BlastTabularParserTest [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: 0.1 s - in org.biojava.nbio.core.sequence.SequenceViewTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 s - in org.biojava.nbio.core.sequence.SequenceViewTest [INFO] Running org.biojava.nbio.core.sequence.ChromosomeSequenceTest 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: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.308 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest +[INFO] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.246 s - in org.biojava.nbio.core.sequence.ChromosomeSequenceTest [INFO] Running org.biojava.nbio.core.sequence.ProteinSequenceTest 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: 0.384 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 s - in org.biojava.nbio.core.sequence.ProteinSequenceTest [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: 0.128 s - in org.biojava.nbio.core.sequence.JoiningSequenceReaderTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 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: 0.16 s - in org.biojava.nbio.core.sequence.TestSequenceEquals +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 s - in org.biojava.nbio.core.sequence.TestSequenceEquals [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: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.024 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest +[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.351 s - in org.biojava.nbio.core.sequence.MultipleSequenceAlignmentTest [INFO] Running org.biojava.nbio.core.sequence.TranscriptSequenceTest 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: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.624 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.18 s - in org.biojava.nbio.core.sequence.TranscriptSequenceTest [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: 0.232 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 s - in org.biojava.nbio.core.sequence.compound.AmbiguityDNACompoundTest [INFO] Running org.biojava.nbio.core.sequence.ExonSequenceTest 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: 0.412 s - in org.biojava.nbio.core.sequence.ExonSequenceTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.core.sequence.ExonSequenceTest [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: 0.55 s - in org.biojava.nbio.core.sequence.DNATest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 s - in org.biojava.nbio.core.sequence.DNATest [INFO] Running org.biojava.nbio.core.sequence.ExonComparatorTest 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: 0.428 s - in org.biojava.nbio.core.sequence.ExonComparatorTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 s - in org.biojava.nbio.core.sequence.ExonComparatorTest [INFO] Running org.biojava.nbio.core.sequence.RNASequenceTest 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: 0.784 s - in org.biojava.nbio.core.sequence.RNASequenceTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.68 s - in org.biojava.nbio.core.sequence.RNASequenceTest [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: 0.236 s - in org.biojava.nbio.core.sequence.EditSequenceTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 s - in org.biojava.nbio.core.sequence.EditSequenceTest [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: 2.696 s - in org.biojava.nbio.core.sequence.TranslationTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.855 s - in org.biojava.nbio.core.sequence.TranslationTest [INFO] Running org.biojava.nbio.core.sequence.GeneSequenceTest 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: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.636 s - in org.biojava.nbio.core.sequence.GeneSequenceTest +[WARNING] Tests run: 11, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.459 s - in org.biojava.nbio.core.sequence.GeneSequenceTest [INFO] Running org.biojava.nbio.core.sequence.TaxonomyIDTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.335 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.core.sequence.TaxonomyIDTest [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: 0.188 s - in org.biojava.nbio.core.sequence.views.WindowViewTests +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 s - in org.biojava.nbio.core.sequence.views.WindowViewTests [INFO] Running org.biojava.nbio.core.sequence.StrandTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.452 s - in org.biojava.nbio.core.sequence.StrandTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 s - in org.biojava.nbio.core.sequence.StrandTest [INFO] Running org.biojava.nbio.core.sequence.location.LocationParserTest -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.076 s - in org.biojava.nbio.core.sequence.location.LocationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.018 s - in org.biojava.nbio.core.sequence.location.LocationParserTest [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: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.312 s - in org.biojava.nbio.core.sequence.location.InsdcParserTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.696 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: 0.24 s - in org.biojava.nbio.core.sequence.location.LocationTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in 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] Running org.biojava.nbio.core.sequence.location.TargetedLocationParserTest -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 s - in org.biojava.nbio.core.sequence.location.TargetedLocationParserTest [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: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.168 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.72 s - in org.biojava.nbio.core.sequence.io.GenbankWriterTest [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: 0.128 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.076 s - in org.biojava.nbio.core.sequence.io.GenericFastaHeaderParserTest [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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.997 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.553 s - in org.biojava.nbio.core.sequence.io.GenbankReaderTest [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: 2.148 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.052 s - in org.biojava.nbio.core.sequence.io.FastaWriterTest [INFO] Running org.biojava.nbio.core.sequence.io.embl.EmblReaderTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.203 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.biojava.nbio.core.sequence.io.embl.EmblReaderTest [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: 0.755 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 s - in org.biojava.nbio.core.sequence.io.FastaReaderTest [INFO] Running org.biojava.nbio.core.sequence.io.FastaGeneWriterTest 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.core.sequence.io.FastaGeneWriterTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 s - in org.biojava.nbio.core.sequence.io.FastaGeneWriterTest [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: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.464 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.biojava.nbio.core.sequence.io.CasePreservingProteinSequenceCreatorTest [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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.383 s - in org.biojava.nbio.core.sequence.io.ABITracerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.086 s - in org.biojava.nbio.core.sequence.io.ABITracerTest [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: 0.768 s - in org.biojava.nbio.core.sequence.io.GenbankCookbookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.144 s - in 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] Running org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest -[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReaderTest +[INFO] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.177 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: 2.916 s - in org.biojava.nbio.core.sequence.loader.SimpleGenbankProxySequenceReaderTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.675 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: 0.156 s - in org.biojava.nbio.core.util.TestUncompressInputStream +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 s - in org.biojava.nbio.core.util.TestUncompressInputStream [INFO] Running org.biojava.nbio.core.util.XMLHelperTest 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: 2.884 s - in org.biojava.nbio.core.util.XMLHelperTest +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.601 s - in org.biojava.nbio.core.util.XMLHelperTest [INFO] Running org.biojava.nbio.core.util.StringManipulationHelperTest 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: 1.015 s - in org.biojava.nbio.core.util.StringManipulationHelperTest +[INFO] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 s - in org.biojava.nbio.core.util.StringManipulationHelperTest [INFO] Running org.biojava.nbio.core.util.PrettyXMLWriterTest 22 @@ -12703,38 +12746,38 @@ 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: 0.524 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 s - in org.biojava.nbio.core.util.PrettyXMLWriterTest [INFO] Running org.biojava.nbio.core.util.CRC64ChecksumTest -[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.684 s - in org.biojava.nbio.core.util.CRC64ChecksumTest +[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.209 s - in org.biojava.nbio.core.util.CRC64ChecksumTest [INFO] Running org.biojava.nbio.core.util.FlatFileCacheTest 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: 0.623 s - in org.biojava.nbio.core.util.FlatFileCacheTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 s - in org.biojava.nbio.core.util.FlatFileCacheTest [INFO] Running org.biojava.nbio.core.util.SingleLinkageClustererTest 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: 0.536 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.516 s - in org.biojava.nbio.core.util.SingleLinkageClustererTest [INFO] Running org.biojava.nbio.core.util.SoftHashMapTest 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: 0.344 s - in org.biojava.nbio.core.util.SoftHashMapTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.18 s - in org.biojava.nbio.core.util.SoftHashMapTest [INFO] Running org.biojava.nbio.core.util.EqualsTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.46 s - in org.biojava.nbio.core.util.EqualsTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.38 s - in org.biojava.nbio.core.util.EqualsTest [INFO] Running org.biojava.nbio.core.util.FileDownloadUtilsTest 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: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.644 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest +[WARNING] Tests run: 18, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 2.916 s - in org.biojava.nbio.core.util.FileDownloadUtilsTest [INFO] Running org.biojava.nbio.core.util.SequenceToolsTest 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: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.14 s - in org.biojava.nbio.core.util.SequenceToolsTest +[WARNING] Tests run: 21, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.143 s - in org.biojava.nbio.core.util.SequenceToolsTest [INFO] Running org.biojava.nbio.core.util.HashcoderTest -[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.464 s - in org.biojava.nbio.core.util.HashcoderTest +[INFO] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.604 s - in org.biojava.nbio.core.util.HashcoderTest [INFO] [INFO] Results: [INFO] @@ -12785,76 +12828,76 @@ 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: 0.623 s - in org.biojava.nbio.phylo.TestForesterWrapper +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 s - in org.biojava.nbio.phylo.TestForesterWrapper [INFO] Running org.biojava.nbio.phylo.TestDistanceTreeEvaluator 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: 0.65 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 s - in org.biojava.nbio.phylo.TestDistanceTreeEvaluator [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: 0.768 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.485 s - in org.biojava.nbio.alignment.FractionalIdentityScorerTest [INFO] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest -[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.436 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.394 s - in org.biojava.nbio.alignment.SimpleGapPenaltyTest [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: 0.67 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.453 s - in org.biojava.nbio.alignment.FractionalSimilarityScorerTest [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: 0.648 s - in org.biojava.nbio.alignment.io.TestStockholmParser +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.277 s - in org.biojava.nbio.alignment.io.TestStockholmParser [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: 1.492 s - in org.biojava.nbio.alignment.NeedlemanWunschTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.897 s - in org.biojava.nbio.alignment.NeedlemanWunschTest [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: 0.944 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.664 s - in org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [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: 0.749 s - in org.biojava.nbio.alignment.GuideTreeTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.4 s - in org.biojava.nbio.alignment.GuideTreeTest [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: 0.728 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.648 s - in org.biojava.nbio.alignment.aaindex.TestAAINDEXLoading [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: 0.763 s - in org.biojava.nbio.alignment.SmithWatermanTest +[INFO] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.biojava.nbio.alignment.SmithWatermanTest [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: 0.388 s - in org.biojava.nbio.alignment.SimpleProfilePairTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.348 s - in org.biojava.nbio.alignment.SimpleProfilePairTest [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: 0.716 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [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: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.393 s - in org.biojava.nbio.alignment.TestDNAAlignment +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.9 s - in org.biojava.nbio.alignment.TestDNAAlignment [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: 0.736 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest +[INFO] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.619 s - in org.biojava.nbio.alignment.routines.GuanUberbacherTest [INFO] Running org.biojava.nbio.alignment.routines.AlignerHelperTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.484 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.28 s - in org.biojava.nbio.alignment.routines.AlignerHelperTest [INFO] Running org.biojava.nbio.alignment.TestSubOptimalMSA SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation @@ -12864,7 +12907,7 @@ 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: 0.819 s - in org.biojava.nbio.alignment.LocalAlignmentTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.476 s - in org.biojava.nbio.alignment.LocalAlignmentTest [INFO] [INFO] Results: [INFO] @@ -12896,88 +12939,88 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.Test2JA5 -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.072 s - in org.biojava.nbio.structure.Test2JA5 +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.023 s - in org.biojava.nbio.structure.Test2JA5 [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: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.292 s - in org.biojava.nbio.structure.SourceCompoundTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.608 s - in org.biojava.nbio.structure.SourceCompoundTest [INFO] Running org.biojava.nbio.structure.TestVeryLongFileName 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: 0.288 s - in org.biojava.nbio.structure.TestVeryLongFileName +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.247 s - in org.biojava.nbio.structure.TestVeryLongFileName [INFO] Running org.biojava.nbio.structure.chem.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: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.934 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.063 s - in org.biojava.nbio.structure.chem.TestDownloadChemCompProvider [INFO] Running org.biojava.nbio.structure.ResidueNumberTest -[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 s - in org.biojava.nbio.structure.ResidueNumberTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 s - in org.biojava.nbio.structure.ResidueNumberTest [INFO] Running org.biojava.nbio.structure.TestDNAAlignment -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.TestDNAAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.06 s - in org.biojava.nbio.structure.TestDNAAlignment [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: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 2.896 s - in org.biojava.nbio.structure.TestAtomCache +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 2.888 s - in org.biojava.nbio.structure.TestAtomCache [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: 15.829 s - in org.biojava.nbio.structure.Test4hhb +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.31 s - in org.biojava.nbio.structure.Test4hhb [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: 0.424 s - in org.biojava.nbio.structure.TestStructureImpl +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.476 s - in org.biojava.nbio.structure.TestStructureImpl [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: 3.336 s - in org.biojava.nbio.structure.ChemCompTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 4.804 s - in org.biojava.nbio.structure.ChemCompTest [INFO] Running org.biojava.nbio.structure.AtomPositionMapTest -[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.014 s - in org.biojava.nbio.structure.AtomPositionMapTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.086 s - in org.biojava.nbio.structure.AtomPositionMapTest [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: 8.885 s - in org.biojava.nbio.structure.TestStructureSerialization +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.216 s - in org.biojava.nbio.structure.TestStructureSerialization [INFO] Running org.biojava.nbio.structure.TestBioAssemblyIdentifier -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.054 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.084 s - in org.biojava.nbio.structure.TestBioAssemblyIdentifier [INFO] Running org.biojava.nbio.structure.TestPdbId [1ABC, PDB_00011ABC, 2ABC, 1ABA, 1100] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] [1100, 1ABA, 1ABC, 2ABC, PDB_00011ABC] -[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.492 s - in org.biojava.nbio.structure.TestPdbId +[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.623 s - in org.biojava.nbio.structure.TestPdbId [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: 0.328 s - in org.biojava.nbio.structure.ResidueRangeTest +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.628 s - in org.biojava.nbio.structure.ResidueRangeTest [INFO] Running org.biojava.nbio.structure.TestChargeAdder -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.066 s - in org.biojava.nbio.structure.TestChargeAdder +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.059 s - in org.biojava.nbio.structure.TestChargeAdder [INFO] Running org.biojava.nbio.structure.PDBStatusTest -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.038 s - in org.biojava.nbio.structure.PDBStatusTest +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.048 s - in org.biojava.nbio.structure.PDBStatusTest [INFO] Running org.biojava.nbio.structure.ElementTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.068 s - in org.biojava.nbio.structure.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 s - in org.biojava.nbio.structure.ElementTest [INFO] Running org.biojava.nbio.structure.TestExperimentalTechniques -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.052 s - in org.biojava.nbio.structure.TestExperimentalTechniques +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.043 s - in org.biojava.nbio.structure.TestExperimentalTechniques [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: 0.336 s - in org.biojava.nbio.structure.TestCalc +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.596 s - in org.biojava.nbio.structure.TestCalc [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: 3.22 s - in org.biojava.nbio.structure.TestEntityResIndexMapping +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 3.7 s - in org.biojava.nbio.structure.TestEntityResIndexMapping [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: 1.817 s - in org.biojava.nbio.structure.HetatomImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 s - in org.biojava.nbio.structure.HetatomImplTest [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 @@ -12988,260 +13031,260 @@ - 5.477225575051661 Interface - 5.477225575051661 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.structure.contact.TestInterfaceFinder +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.58 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: 0.06 s - in org.biojava.nbio.structure.contact.TestContactCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.048 s - in org.biojava.nbio.structure.contact.TestContactCalc [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: 11.408 s - in org.biojava.nbio.structure.TestEntityHeuristics +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.904 s - in org.biojava.nbio.structure.TestEntityHeuristics [INFO] Running org.biojava.nbio.structure.TestKeywords 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: 6.748 s - in org.biojava.nbio.structure.TestKeywords +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.147 s - in org.biojava.nbio.structure.TestKeywords [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: 8.575 s - in org.biojava.nbio.structure.PdbFileFormat30Test +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.292 s - in org.biojava.nbio.structure.PdbFileFormat30Test [INFO] Running org.biojava.nbio.structure.TestLoadStructureFromURL -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.02 s - in org.biojava.nbio.structure.TestLoadStructureFromURL +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.019 s - in org.biojava.nbio.structure.TestLoadStructureFromURL [INFO] Running org.biojava.nbio.structure.redmine.Test1DARSeqAlign -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.04 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.012 s - in org.biojava.nbio.structure.redmine.Test1DARSeqAlign [INFO] Running org.biojava.nbio.structure.TestParsingCalcium -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.055 s - in org.biojava.nbio.structure.TestParsingCalcium +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.024 s - in org.biojava.nbio.structure.TestParsingCalcium [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. -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.215 s - in org.biojava.nbio.structure.geometry.TestSuperPositionQCP +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.127 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: 0.096 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.056 s - in org.biojava.nbio.structure.geometry.TestUnitQuaternions [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: 9.095 s - in org.biojava.nbio.structure.geometry.TestSuperPosition +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.388 s - in org.biojava.nbio.structure.geometry.TestSuperPosition [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: 0.228 s - in org.biojava.nbio.structure.SiteTest +[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 s - in org.biojava.nbio.structure.SiteTest [INFO] Running org.biojava.nbio.structure.TestCloning -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.054 s - in org.biojava.nbio.structure.TestCloning +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.025 s - in org.biojava.nbio.structure.TestCloning [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: 0.594 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.6 s - in org.biojava.nbio.structure.cluster.TestSubunitCluster [INFO] Running org.biojava.nbio.structure.cluster.TestSubunitExtractor -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.06 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.02 s - in org.biojava.nbio.structure.cluster.TestSubunitExtractor [INFO] Running org.biojava.nbio.structure.TestStructureCrossReferences [WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.044 s - in org.biojava.nbio.structure.TestStructureCrossReferences [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalCell -[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.structure.xtal.TestCrystalCell +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 s - in org.biojava.nbio.structure.xtal.TestCrystalCell [INFO] Running org.biojava.nbio.structure.xtal.TestCrystalInfo -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.044 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.037 s - in org.biojava.nbio.structure.xtal.TestCrystalInfo [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: 19.552 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 10.564 s - in org.biojava.nbio.structure.xtal.TestInterfaceClustering [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: 3.1 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.04 s - in org.biojava.nbio.structure.xtal.TestSpaceGroup [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: 0.415 s - in org.biojava.nbio.structure.align.ce.CeCPMainTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.188 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: 0.04 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.009 s - in org.biojava.nbio.structure.align.ce.TestSmallAlignment [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: 0.441 s - in org.biojava.nbio.structure.align.util.AtomCacheTest +[WARNING] Tests run: 10, Failures: 0, Errors: 0, Skipped: 8, Time elapsed: 0.132 s - in org.biojava.nbio.structure.align.util.AtomCacheTest [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: 0.139 s - in org.biojava.nbio.structure.align.util.RotationAxisTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.107 s - in org.biojava.nbio.structure.align.util.RotationAxisTest [INFO] Running org.biojava.nbio.structure.align.TestAlignmentConsistency [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 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: 0.248 s - in org.biojava.nbio.structure.align.client.TestStructureName +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.24 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: 0.32 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 s - in org.biojava.nbio.structure.align.multiple.TestAFPChainConversion [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter -[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.039 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 6, Time elapsed: 0.034 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentWriter [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.112 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.095 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentTools [INFO] Running org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.082 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.024 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentXMLParser [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: 0.429 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 s - in org.biojava.nbio.structure.align.multiple.util.TestMultipleAlignmentScorer [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: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.152 s - in org.biojava.nbio.structure.asa.TestAsaCalc +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.148 s - in org.biojava.nbio.structure.asa.TestAsaCalc [INFO] Running org.biojava.nbio.structure.TestBond -[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.061 s - in org.biojava.nbio.structure.TestBond +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 15, Time elapsed: 0.044 s - in org.biojava.nbio.structure.TestBond [INFO] Running org.biojava.nbio.structure.basepairs.TestBasePairParameters -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.032 s - in org.biojava.nbio.structure.basepairs.TestBasePairParameters [INFO] Running org.biojava.nbio.structure.TestNucleotides -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.064 s - in org.biojava.nbio.structure.TestNucleotides +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.015 s - in org.biojava.nbio.structure.TestNucleotides [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: 8.124 s - in org.biojava.nbio.structure.TestURLIdentifier +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.78 s - in org.biojava.nbio.structure.TestURLIdentifier [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: 3.232 s - in org.biojava.nbio.structure.TestAltLocs +[WARNING] Tests run: 15, Failures: 0, Errors: 0, Skipped: 11, Time elapsed: 1.179 s - in org.biojava.nbio.structure.TestAltLocs [INFO] Running org.biojava.nbio.structure.TestAtomIterator [WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.TestAtomIterator [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: 0.18 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.115 s - in org.biojava.nbio.structure.symmetry.utils.TestSymmetryTools [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: 0.239 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.symmetry.internal.TestSingleRefiner [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.152 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 s - in org.biojava.nbio.structure.symmetry.internal.TestSymmetryAxes [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.056 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.036 s - in org.biojava.nbio.structure.symmetry.internal.TestSequenceFunctionOrderDetector [INFO] Running org.biojava.nbio.structure.symmetry.internal.TestCeSymm -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.037 s - in org.biojava.nbio.structure.symmetry.internal.TestCeSymm [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: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.872 s - in org.biojava.nbio.structure.io.TestMMCIFWriting +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.318 s - in org.biojava.nbio.structure.io.TestMMCIFWriting [INFO] Running org.biojava.nbio.structure.io.TestParseOnAsymId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.073 s - in org.biojava.nbio.structure.io.TestParseOnAsymId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestParseOnAsymId [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: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 11.233 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles +[WARNING] Tests run: 14, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 6.176 s - in org.biojava.nbio.structure.io.TestNonDepositedFiles [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFFeatures -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.065 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.04 s - in org.biojava.nbio.structure.io.TestParseMmCIFFeatures [INFO] Running org.biojava.nbio.structure.io.TestTitleParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.084 s - in org.biojava.nbio.structure.io.TestTitleParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.016 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: 0.388 s - in org.biojava.nbio.structure.io.TestDBRefParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.22 s - in org.biojava.nbio.structure.io.TestDBRefParsing [INFO] Running org.biojava.nbio.structure.io.TestHardBioUnits -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.068 s - in org.biojava.nbio.structure.io.TestHardBioUnits +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.028 s - in org.biojava.nbio.structure.io.TestHardBioUnits [INFO] Running org.biojava.nbio.structure.io.TestSiftsParsing -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.068 s - in org.biojava.nbio.structure.io.TestSiftsParsing +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.039 s - in org.biojava.nbio.structure.io.TestSiftsParsing [INFO] Running org.biojava.nbio.structure.io.TestQuaternaryStructureProviders -[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.064 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 7, Time elapsed: 0.043 s - in org.biojava.nbio.structure.io.TestQuaternaryStructureProviders [INFO] Running org.biojava.nbio.structure.io.TestParseMmCIFLigands -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.045 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.044 s - in org.biojava.nbio.structure.io.TestParseMmCIFLigands [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: 2.301 s - in org.biojava.nbio.structure.io.TestShortLines +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.152 s - in org.biojava.nbio.structure.io.TestShortLines [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: 7.732 s - in org.biojava.nbio.structure.io.TestHeaderOnly +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 3.484 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: 0.06 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest +[WARNING] Tests run: 5, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.FastaAFPChainConverterTest [INFO] Running org.biojava.nbio.structure.io.TestURLBasedFileParsing -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.052 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.044 s - in org.biojava.nbio.structure.io.TestURLBasedFileParsing [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: 6.844 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.596 s - in org.biojava.nbio.structure.io.cif.CifFileConsumerImplTest [INFO] Running org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.072 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.055 s - in org.biojava.nbio.structure.io.TestWriteLargeCoordinatePDB [INFO] Running org.biojava.nbio.structure.io.TestMMcifOrganismParsing -[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.08 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 3, Time elapsed: 0.01 s - in org.biojava.nbio.structure.io.TestMMcifOrganismParsing [INFO] Running org.biojava.nbio.structure.io.StructureSequenceMatcherTest -[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.06 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest +[WARNING] Tests run: 4, Failures: 0, Errors: 0, Skipped: 4, Time elapsed: 0.068 s - in org.biojava.nbio.structure.io.StructureSequenceMatcherTest [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: 5.715 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles +[WARNING] Tests run: 7, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 5.111 s - in org.biojava.nbio.structure.io.TestDifficultMmCIFFiles [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: 2.265 s - in org.biojava.nbio.structure.io.mmcif.TestChemCompProvider +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.564 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: 0.06 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.mmcif.TestEntityNameAndType [INFO] Running org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.068 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.io.mmcif.TestParseInternalChainId [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: 6.644 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.548 s - in org.biojava.nbio.structure.io.mmcif.TestParseMmcifHeader [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: 6.643 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.084 s - in org.biojava.nbio.structure.io.mmcif.TestMmcifV5Changes [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: 6.843 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.652 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureWriter [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.077 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfRoundTrip +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.012 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: 0.067 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.013 s - in org.biojava.nbio.structure.io.mmtf.TestBondFinding [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: 18.046 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader +[WARNING] Tests run: 3, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1.84 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfStructureReader [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: 0.684 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils +[WARNING] Tests run: 16, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.228 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfUtils [INFO] Running org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.068 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.io.mmtf.TestMmtfPerformance [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: 0.368 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 s - in org.biojava.nbio.structure.io.sifts.SiftsChainToUniprotMappingTest [INFO] Running org.biojava.nbio.structure.secstruc.TestSecStrucCalc -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.044 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.032 s - in org.biojava.nbio.structure.secstruc.TestSecStrucCalc [INFO] Running org.biojava.nbio.structure.secstruc.TestDSSPParser -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.076 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.015 s - in org.biojava.nbio.structure.secstruc.TestDSSPParser [INFO] [INFO] Results: [INFO] @@ -13289,20 +13332,20 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.structure.gui.RenderStyleTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 s - in org.biojava.nbio.structure.gui.RenderStyleTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 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: 0.366 s - in org.biojava.nbio.structure.gui.TestAtomInfo +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.14 s - in org.biojava.nbio.structure.gui.TestAtomInfo [INFO] Running org.biojava.nbio.structure.gui.StructureViewerTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.416 s - in org.biojava.nbio.structure.gui.StructureViewerTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 s - in org.biojava.nbio.structure.gui.StructureViewerTest [INFO] Running org.biojava.nbio.structure.gui.ViewerTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 s - in org.biojava.nbio.structure.gui.ViewerTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.092 s - in org.biojava.nbio.structure.gui.ViewerTest [INFO] Running org.biojava.nbio.structure.gui.JmolViewerImplTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.36 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.272 s - in org.biojava.nbio.structure.gui.JmolViewerImplTest [INFO] Running org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator -[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.3 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.296 s - in org.biojava.nbio.structure.symmetry.TestJmolSymmetryScriptGenerator [INFO] [INFO] Results: [INFO] @@ -13331,50 +13374,50 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.genome.TestIssue355 -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.357 s - in org.biojava.nbio.genome.TestIssue355 +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.267 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: 0.436 s - in org.biojava.nbio.genome.FeatureListTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 s - in org.biojava.nbio.genome.FeatureListTest [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: 0.319 s - in org.biojava.nbio.genome.TestChromosomeMappingTools +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.488 s - in org.biojava.nbio.genome.TestChromosomeMappingTools [INFO] Running org.biojava.nbio.genome.TestLocation -[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 s - in org.biojava.nbio.genome.TestLocation +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.428 s - in org.biojava.nbio.genome.TestLocation [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: 2.969 s - in org.biojava.nbio.genome.GeneFeatureHelperTest +[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.385 s - in org.biojava.nbio.genome.GeneFeatureHelperTest [INFO] Running org.biojava.nbio.genome.TestGenomeMapping -[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.368 s - in org.biojava.nbio.genome.TestGenomeMapping +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.333 s - in org.biojava.nbio.genome.TestGenomeMapping [INFO] Running org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest -[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.327 s - in org.biojava.nbio.genome.io.fastq.StreamingFastqParserTest [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: 0.816 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest +[INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.867 s - in org.biojava.nbio.genome.io.fastq.FastqToolsTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.568 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.432 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.677 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.445 s - in org.biojava.nbio.genome.io.fastq.SangerFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.ConvertTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.008 s - in org.biojava.nbio.genome.io.fastq.ConvertTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.994 s - in org.biojava.nbio.genome.io.fastq.ConvertTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.576 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.441 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqWriterTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqBuilderTest -[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.465 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest +[INFO] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.449 s - in org.biojava.nbio.genome.io.fastq.FastqBuilderTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqVariantTest -[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest +[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.485 s - in org.biojava.nbio.genome.io.fastq.FastqVariantTest [INFO] Running org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.972 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.74 s - in org.biojava.nbio.genome.io.fastq.IlluminaFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.FastqTest -[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.444 s - in org.biojava.nbio.genome.io.fastq.FastqTest +[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.356 s - in org.biojava.nbio.genome.io.fastq.FastqTest [INFO] Running org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest -[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.94 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest +[INFO] Tests run: 29, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.683 s - in org.biojava.nbio.genome.io.fastq.SangerFastqReaderTest [INFO] Running org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest -[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.844 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest +[INFO] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.607 s - in org.biojava.nbio.genome.io.fastq.SolexaFastqReaderTest [INFO] [INFO] Results: [INFO] @@ -13403,19 +13446,19 @@ [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: 0.46 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.236 s - in org.biojava.nbio.protmod.phosphosite.TestAcetylation [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: 2.738 s - in org.biojava.nbio.protmod.structure.ModifiedCompoundSerializationTest +[WARNING] Tests run: 6, Failures: 0, Errors: 0, Skipped: 5, Time elapsed: 1.777 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: 0.412 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest +[WARNING] Tests run: 2, Failures: 0, Errors: 0, Skipped: 2, Time elapsed: 0.268 s - in org.biojava.nbio.protmod.structure.ProteinModificationParserTest [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: 1.992 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.78 s - in org.biojava.nbio.protmod.structure.ProteinModificationRegistryTest [INFO] [INFO] Results: [INFO] @@ -13444,7 +13487,7 @@ [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: 0.428 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan +[WARNING] Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.364 s - in org.biojava.nbio.ws.hmmer.TestRemoteHmmerScan [INFO] [INFO] Results: [INFO] @@ -13473,12 +13516,12 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.biojava.nbio.ronn.NonstandardProteinCompoundTest -[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.3 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.193 s - in org.biojava.nbio.ronn.NonstandardProteinCompoundTest [INFO] Running org.biojava.nbio.ronn.JronnTest 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: 15.932 s - in org.biojava.nbio.ronn.JronnTest +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 13.195 s - in org.biojava.nbio.ronn.JronnTest [INFO] [INFO] Results: [INFO] @@ -13533,37 +13576,37 @@ 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: 2.3 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.44 s - in org.biojava.nbio.aaproperties.GenbankCommandPromptTest [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: 0.323 s - in org.biojava.nbio.aaproperties.profeat.CookBookTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.493 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: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.417 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest +[INFO] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.135 s - in org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [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: 2.488 s - in org.biojava.nbio.aaproperties.xml.AminoAcidTest +[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.786 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: 2.508 s - in org.biojava.nbio.aaproperties.xml.ElementTest +[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.087 s - in org.biojava.nbio.aaproperties.xml.ElementTest [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: 0.38 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.458 s - in org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [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: 1.908 s - in org.biojava.nbio.aaproperties.CookBookTest +[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.823 s - in org.biojava.nbio.aaproperties.CookBookTest [INFO] [INFO] Results: [INFO] @@ -13614,17 +13657,17 @@ 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: 0.811 s - in org.biojava.nbio.ontology.TestParseOBO +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.946 s - in org.biojava.nbio.ontology.TestParseOBO [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: 0.98 s - in org.biojava.nbio.ontology.TestParseSBO +[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.038 s - in org.biojava.nbio.ontology.TestParseSBO [INFO] Running org.biojava.nbio.ontology.TestOboFileParsing 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: 1.143 s - in org.biojava.nbio.ontology.TestOboFileParsing +[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.284 s - in org.biojava.nbio.ontology.TestOboFileParsing [INFO] [INFO] Results: [INFO] @@ -13652,26 +13695,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 0.006 s] -[INFO] biojava-core ....................................... SUCCESS [10:33 min] -[INFO] biojava-forester ................................... SUCCESS [ 0.323 s] -[INFO] biojava-alignment .................................. SUCCESS [03:10 min] -[INFO] biojava-structure .................................. SUCCESS [20:02 min] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 3.637 s] -[INFO] biojava-structure-gui .............................. SUCCESS [01:01 min] +[INFO] biojava ............................................ SUCCESS [ 0.007 s] +[INFO] biojava-core ....................................... SUCCESS [09:52 min] +[INFO] biojava-forester ................................... SUCCESS [ 0.858 s] +[INFO] biojava-alignment .................................. SUCCESS [03:00 min] +[INFO] biojava-structure .................................. SUCCESS [17:53 min] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 1.697 s] +[INFO] biojava-structure-gui .............................. SUCCESS [01:00 min] [INFO] biojava-genome ..................................... SUCCESS [03:00 min] -[INFO] biojava-modfinder .................................. SUCCESS [ 40.581 s] -[INFO] biojava-ws ......................................... SUCCESS [ 10.537 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 30.151 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 40.279 s] +[INFO] biojava-ws ......................................... SUCCESS [ 10.423 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 30.121 s] [INFO] biojava-aa-prop .................................... SUCCESS [01:20 min] -[INFO] biojava-survival ................................... SUCCESS [ 0.081 s] -[INFO] biojava-ontology ................................... SUCCESS [ 30.184 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.272 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.399 s] +[INFO] biojava-ontology ................................... SUCCESS [ 31.531 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 2.856 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 41:05 min -[INFO] Finished at: 2024-05-27T06:13:57-12:00 +[INFO] Total time: 38:06 min +[INFO] Finished at: 2023-04-26T02:48:17+14:00 [INFO] ------------------------------------------------------------------------  create-stamp debian/debhelper-build-stamp dh_prep @@ -13888,26 +13931,26 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for biojava 6.1.0: [INFO] -[INFO] biojava ............................................ SUCCESS [ 1.670 s] -[INFO] biojava-core ....................................... SUCCESS [ 0.666 s] -[INFO] biojava-forester ................................... SUCCESS [ 0.640 s] -[INFO] biojava-alignment .................................. SUCCESS [ 0.324 s] -[INFO] biojava-structure .................................. SUCCESS [ 0.596 s] -[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.236 s] -[INFO] biojava-structure-gui .............................. SUCCESS [ 0.413 s] -[INFO] biojava-genome ..................................... SUCCESS [ 0.212 s] -[INFO] biojava-modfinder .................................. SUCCESS [ 0.260 s] -[INFO] biojava-ws ......................................... SUCCESS [ 0.259 s] -[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.269 s] -[INFO] biojava-aa-prop .................................... SUCCESS [ 0.172 s] -[INFO] biojava-survival ................................... SUCCESS [ 0.188 s] -[INFO] biojava-ontology ................................... SUCCESS [ 0.248 s] -[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.156 s] +[INFO] biojava ............................................ SUCCESS [ 2.202 s] +[INFO] biojava-core ....................................... SUCCESS [ 0.630 s] +[INFO] biojava-forester ................................... SUCCESS [ 0.960 s] +[INFO] biojava-alignment .................................. SUCCESS [ 0.247 s] +[INFO] biojava-structure .................................. SUCCESS [ 1.096 s] +[INFO] biojava-jcolorbrewer ............................... SUCCESS [ 0.271 s] +[INFO] biojava-structure-gui .............................. SUCCESS [ 0.880 s] +[INFO] biojava-genome ..................................... SUCCESS [ 0.284 s] +[INFO] biojava-modfinder .................................. SUCCESS [ 0.272 s] +[INFO] biojava-ws ......................................... SUCCESS [ 0.224 s] +[INFO] biojava-protein-disorder ........................... SUCCESS [ 0.344 s] +[INFO] biojava-aa-prop .................................... SUCCESS [ 0.248 s] +[INFO] biojava-survival ................................... SUCCESS [ 0.327 s] +[INFO] biojava-ontology ................................... SUCCESS [ 0.224 s] +[INFO] biojava-protein-comparison-tool .................... SUCCESS [ 0.207 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 7.396 s -[INFO] Finished at: 2024-05-27T06:14:19-12:00 +[INFO] Total time: 9.818 s +[INFO] Finished at: 2023-04-26T02:48:49+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibbiojava6-java --javadoc --base-directory=/build/biojava6-live-6.1.0\+dfsg --non-explore Analysing pom.xml... @@ -14114,7 +14157,7 @@ jh_installjavadoc debian/rules override_dh_installdocs make[1]: Entering directory '/build/biojava6-live-6.1.0+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 \ @@ -14152,12 +14195,14 @@ 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/4041559/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4041559/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/135845 and its subdirectories -I: Current time: Mon May 27 06:23:53 -12 2024 -I: pbuilder-time-stamp: 1716834233 +I: removing directory /srv/workspace/pbuilder/4041559 and its subdirectories +I: Current time: Wed Apr 26 02:56:56 +14 2023 +I: pbuilder-time-stamp: 1682427416