Diff of the two buildlogs: -- --- b1/build.log 2021-08-13 22:48:17.715102313 +0000 +++ b2/build.log 2021-08-13 23:00:01.920744244 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 13 10:37:54 -12 2021 -I: pbuilder-time-stamp: 1628894274 +I: Current time: Sat Aug 14 12:49:14 +14 2021 +I: pbuilder-time-stamp: 1628894954 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./biojava4-live_4.2.12+dfsg-3.1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.Q6S4UCw1/trustedkeys.kbx': General error -gpgv: Signature made Mon Jul 13 07:29:24 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.NMwnYb6u/trustedkeys.kbx': General error +gpgv: Signature made Tue Jul 14 09:29:24 2020 +14 gpgv: using RSA key 58B66D48736BE93B052DE6729C5C99EB05BD750A gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biojava4-live_4.2.12+dfsg-3.1.dsc @@ -35,135 +35,169 @@ dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21715/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2657/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2657/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2657/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='1cb17b4eb806462e9d5c8e812767557b' - 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='21715' - PS1='# ' - PS2='> ' + INVOCATION_ID=1a29e722f5cc4b5c98daa67711a99b9c + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2657 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/pbuilderrc_eBGw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/pbuilderrc_tEpP --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.I27oqKZ04L/b2 --logfile b2/build.log --extrapackages usrmerge biojava4-live_4.2.12+dfsg-3.1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux jtx1c 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-8-armmp-lpae #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Jul 28 07:09 more - -rwsr-xr-x 1 root root 34400 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 9824 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 11 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Jul 28 07:09 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/21715/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Jul 29 09:09 more + -rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 14 12:49 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 10 23:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Jul 29 09:09 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/2657/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -478,7 +512,7 @@ Get: 219 http://deb.debian.org/debian bullseye/main armhf libvecmath-java all 1.5.2-7 [97.0 kB] Get: 220 http://deb.debian.org/debian bullseye/main armhf libxmlunit-java all 1.6-2 [100 kB] Get: 221 http://deb.debian.org/debian bullseye/main armhf rdfind armhf 1.4.1-1+b2 [37.2 kB] -Fetched 301 MB in 42s (7100 kB/s) +Fetched 301 MB in 32s (9516 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19398 files and directories currently installed.) @@ -1399,135 +1433,135 @@ Setting up javahelper (0.78) ... Setting up ca-certificates-java (20190909) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:Certigna_Root_CA.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:emSign_Root_CA_-_C1.pem +Adding debian:Secure_Global_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem -Adding debian:Security_Communication_RootCA2.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:TrustCor_ECA-1.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:GTS_Root_R4.pem +Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:XRamp_Global_CA_Root.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:ACCVRAIZ1.pem +Adding debian:GTS_Root_R2.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:UCA_Global_G2_Root.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:COMODO_ECC_Certification_Authority.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:EC-ACC.pem Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:AffirmTrust_Commercial.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:GTS_Root_R2.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:Certigna_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:emSign_ECC_Root_CA_-_C3.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:UCA_Global_G2_Root.pem -Adding debian:SecureTrust_CA.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:Starfield_Class_2_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:UCA_Extended_Validation_Root.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:Amazon_Root_CA_3.pem Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:GTS_Root_R4.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:Certum_Trusted_Network_CA_2.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:GTS_Root_R3.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:AffirmTrust_Premium.pem -Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem +Adding debian:Trustwave_Global_Certification_Authority.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:Secure_Global_CA.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:emSign_Root_CA_-_C1.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:certSIGN_Root_CA_G2.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:TWCA_Global_Root_CA.pem -Adding debian:AffirmTrust_Networking.pem +Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:AffirmTrust_Premium.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:Trustwave_Global_Certification_Authority.pem -Adding debian:Izenpe.com.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:Certigna.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:SecureTrust_CA.pem Adding debian:GTS_Root_R1.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:EC-ACC.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:Certigna.pem +Adding debian:GTS_Root_R3.pem Adding debian:GlobalSign_Root_CA.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:Hongkong_Post_Root_CA_3.pem +Adding debian:Izenpe.com.pem done. Setting up junit4 (4.13.1-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... @@ -1557,9 +1591,42 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (94.9 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 38313 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-3.1_source.changes +hostname: Name or service not known +I: Running cd /build/biojava4-live-4.2.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biojava4-live_4.2.12+dfsg-3.1_source.changes dpkg-buildpackage: info: source package biojava4-live dpkg-buildpackage: info: source version 4.2.12+dfsg-3.1 dpkg-buildpackage: info: source distribution unstable @@ -1571,8 +1638,8 @@ dh clean --with javahelper jh_clean debian/rules override_dh_clean -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" dh_clean rm -rf build rm -rf dist @@ -1585,15 +1652,15 @@ rm -rf buildtest find . -type f -name \*.java.json-simple \ -exec sh -c 'file={} && mv $file ${file%.json-simple}' \; -print -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» debian/rules build dpkg: warning: --compare-versions used with obsolete relation operator '>' dh build --with javahelper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" dh_auto_configure sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml @@ -1611,11 +1678,11 @@ sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» jh_linkjars debian/rules override_dh_auto_build -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" find . -type f -name \*.java -exec grep -q 'import @JSON_SIMPLE_PACKAGE@' {} \; \ -exec sed -i.json-simple \ -e 's,@JSON_SIMPLE_PACKAGE@,org.json.simple,' \ @@ -1637,7 +1704,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 6 seconds cd biojava-forester && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1653,7 +1720,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 55 seconds +Total time: 34 seconds cd biojava-core && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1671,7 +1738,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 29 seconds +Total time: 18 seconds cd biojava-phylo && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1685,7 +1752,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 6 seconds cd biojava-alignment && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1701,7 +1768,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 10 seconds cd biojava-aa-prop && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1719,7 +1786,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 9 seconds cd biojava-genome && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1735,7 +1802,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 10 seconds cd biojava-sequencing && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1750,7 +1817,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 6 seconds cd biojava-structure && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1768,7 +1835,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 31 seconds +Total time: 33 seconds cd biojava-structure-gui && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1786,7 +1853,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 17 seconds +Total time: 18 seconds cd biojava-modfinder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1820,7 +1887,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 7 seconds cd biojava-protein-disorder && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1836,7 +1903,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 6 seconds +Total time: 7 seconds cd biojava-protein-comparison-tool && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1864,7 +1931,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 5 seconds +Total time: 6 seconds cd biojava-survival && ant jar Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1878,7 +1945,7 @@ [jar] Building jar: /build/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 12 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2171,12 +2238,12 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 1 minute 10 seconds +Total time: 1 minute 12 seconds # rm -rf biojavadoc -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» debian/rules override_dh_auto_test -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -2207,26 +2274,26 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleAlignedSequenceTest - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.165 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.165 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.161 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.161 sec [junit] - [junit] Testcase: testGetIndexOf took 0.075 sec + [junit] Testcase: testGetIndexOf took 0.076 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetNumGaps took 0.001 sec - [junit] Testcase: testGetStart took 0.001 sec - [junit] Testcase: testGetSequenceIndexAt took 0.001 sec + [junit] Testcase: testGetStart took 0 sec + [junit] Testcase: testGetSequenceIndexAt took 0 sec [junit] Testcase: testGetAccession took 0.001 sec - [junit] Testcase: testToString took 0.004 sec + [junit] Testcase: testToString took 0.003 sec [junit] Testcase: testSimpleAlignedSequenceLong took 0.001 sec [junit] Testcase: testCountCompounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.004 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED [junit] Testcase: testGetAsList took 0.005 sec @@ -2235,7 +2302,7 @@ [junit] Testcase: testGetLength took 0.001 sec [junit] Testcase: testIsCircular took 0.001 sec [junit] Testcase: testGetEnd took 0.001 sec - [junit] Testcase: testSimpleAlignedSequenceLocal took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec [junit] Testcase: testGetOverlapCount took 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec @@ -2246,40 +2313,40 @@ [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.004 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.376 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.376 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.342 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.342 sec [junit] - [junit] Testcase: testGetIndexOf took 0.134 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.004 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.004 sec - [junit] Testcase: testToStringInt took 0.022 sec - [junit] Testcase: testToString took 0.003 sec - [junit] Testcase: testToStringFormatted took 0.062 sec + [junit] Testcase: testGetIndexOf took 0.125 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.002 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.003 sec + [junit] Testcase: testToStringInt took 0.02 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testToStringFormatted took 0.063 sec [junit] Testcase: testSimpleProfile took 0.001 sec - [junit] Testcase: testGetSize took 0 sec + [junit] Testcase: testGetSize took 0.001 sec [junit] Testcase: testGetAlignedSequenceS took 0.001 sec - [junit] Testcase: testGetAlignedSequences took 0.002 sec - [junit] Testcase: testGetOriginalSequences took 0 sec + [junit] Testcase: testGetAlignedSequences took 0.001 sec + [junit] Testcase: testGetOriginalSequences took 0.001 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED [junit] Testcase: testGetCompoundAtSInt took 0.001 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.001 sec - [junit] Testcase: testGetIndicesAt took 0.016 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0.015 sec + [junit] Testcase: testGetIndicesAt took 0.01 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.008 sec - [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.004 sec + [junit] Testcase: testGetCompoundAtIntInt took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.001 sec [junit] Testcase: testGetLength took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec [junit] Testcase: testIsCircular took 0 sec [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec @@ -2288,88 +2355,88 @@ [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec [junit] Testcase: testGetCompoundSet took 0.001 sec - [junit] Testcase: testGetCompoundsAt took 0 sec + [junit] Testcase: testGetCompoundsAt took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec - [junit] Testcase: testIterator took 0.001 sec + [junit] Testcase: testIterator took 0.002 sec [junit] Testcase: testGetLastIndexOf took 0.002 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0.001 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.221 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.114 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.142 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetQuery took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetIndexInTargetAt took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec - [junit] Testcase: testGetCompoundInQueryAt took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.003 sec - [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec + [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0.001 sec [junit] Testcase: testGetNumIdenticals took 0.001 sec [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds4 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAt took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0 sec [junit] Testcase: testGetNumSimilars took 0.003 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0 sec [junit] Running org.biojava.nbio.core.search.io.HspTest [junit] Testsuite: org.biojava.nbio.core.search.io.HspTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.165 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.19 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.14 sec + [junit] Testcase: testGetAlignment took 0.16 sec [junit] Testcase: testHashCode took 0 sec - [junit] Testcase: testEquals took 0 sec + [junit] Testcase: testEquals took 0.001 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.69 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.664 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml - [junit] Aug 13, 2021 10:45:46 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Aug 14, 2021 12:57:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Aug 13, 2021 10:45:46 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Aug 14, 2021 12:57:22 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: 135 hits approximately in all results [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testConstructorWithEvalueHspFilter took 0.357 sec + [junit] Testcase: testConstructorWithEvalueHspFilter took 0.358 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2380,8 +2447,8 @@ [junit] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) [junit] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) [junit] - [junit] Testcase: testConstructorWithFactoryGuess took 0.244 sec - [junit] Testcase: testConstructorWithoutFactoryGuess took 0.009 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.258 sec + [junit] Testcase: testConstructorWithoutFactoryGuess took 0.01 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2396,7 +2463,7 @@ BUILD FAILED /build/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed -Total time: 20 seconds +Total time: 19 seconds cd biojava-alignment && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -2411,32 +2478,32 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.alignment.FractionalIdentityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalIdentityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.199 sec [junit] - [junit] Testcase: testGetQuery took 0.122 sec + [junit] Testcase: testGetQuery took 0.115 sec [junit] Testcase: testGetScore took 0.051 sec - [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0.001 sec + [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.002 sec + [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.002 sec [junit] Running org.biojava.nbio.alignment.FractionalSimilarityScorerTest [junit] Testsuite: org.biojava.nbio.alignment.FractionalSimilarityScorerTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.212 sec [junit] - [junit] Testcase: testGetQuery took 0.099 sec - [junit] Testcase: testGetScore took 0.048 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.003 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testGetQuery took 0.119 sec + [junit] Testcase: testGetScore took 0.054 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.004 sec + [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec - [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.003 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.005 sec [junit] Running org.biojava.nbio.alignment.GuideTreeTest [junit] Testsuite: org.biojava.nbio.alignment.GuideTreeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.35 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.389 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -2448,157 +2515,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.244 sec + [junit] Testcase: testGuideTree took 0.265 sec [junit] Testcase: testToString took 0.006 sec [junit] Testcase: testGetScoreMatrix took 0.01 sec - [junit] Testcase: testGetRoot took 0.044 sec + [junit] Testcase: testGetRoot took 0.052 sec [junit] Testcase: testGetSequences took 0.006 sec - [junit] Testcase: testGetDistanceMatrix took 0.005 sec - [junit] Testcase: testGetAllPairsScores took 0.006 sec + [junit] Testcase: testGetDistanceMatrix took 0.006 sec + [junit] Testcase: testGetAllPairsScores took 0.007 sec [junit] Testcase: testIterator took 0.005 sec [junit] Running org.biojava.nbio.alignment.LocalAlignmentTest [junit] Testsuite: org.biojava.nbio.alignment.LocalAlignmentTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.194 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.229 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.174 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.204 sec [junit] Running org.biojava.nbio.alignment.NeedlemanWunschTest [junit] Testsuite: org.biojava.nbio.alignment.NeedlemanWunschTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.589 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.701 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.701 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.099 sec - [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.047 sec - [junit] Testcase: should_align_middle_anchor took 0.064 sec - [junit] Testcase: testGetQuery took 0.005 sec - [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.113 sec + [junit] Testcase: testGetGapPenalty took 0.001 sec + [junit] Testcase: testGetComputationTime took 0.051 sec + [junit] Testcase: should_align_middle_anchor took 0.075 sec + [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetScore took 0.002 sec [junit] Testcase: testNeedlemanWunsch took 0.001 sec [junit] Testcase: should_align_all_anchored took 0.001 sec [junit] Testcase: testGetScoreMatrix took 0.001 sec [junit] Testcase: testGetPair took 0.002 sec [junit] Testcase: should_align_multiple_anchors took 0.001 sec - [junit] Testcase: testAnchoredDNAAlignment took 0.005 sec - [junit] Testcase: testGetProfile took 0.002 sec - [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.007 sec + [junit] Testcase: testGetProfile took 0.003 sec + [junit] Testcase: testGetMinScore took 0.002 sec [junit] Testcase: should_align_ending_anchor took 0.002 sec [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec - [junit] Testcase: testComplex took 0.033 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.027 sec - [junit] Testcase: should_align_starting_anchor took 0.002 sec + [junit] Testcase: testComplex took 0.043 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.029 sec + [junit] Testcase: should_align_starting_anchor took 0.001 sec [junit] Testcase: anchors_should_not_change_score took 0.001 sec - [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetTarget took 0.001 sec [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: testIntOverflowBug took 0.254 sec + [junit] Testcase: testIntOverflowBug took 0.318 sec [junit] Running org.biojava.nbio.alignment.SimpleGapPenaltyTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleGapPenaltyTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec [junit] - [junit] Testcase: testOpenPenalty took 0.007 sec - [junit] Testcase: testType took 0 sec - [junit] Testcase: testExtensionPenalty took 0 sec - [junit] Testcase: testSimpleGapPenaltyShortShort took 0 sec + [junit] Testcase: testOpenPenalty took 0.009 sec + [junit] Testcase: testType took 0.001 sec + [junit] Testcase: testExtensionPenalty took 0.001 sec + [junit] Testcase: testSimpleGapPenaltyShortShort took 0.001 sec [junit] Testcase: testSimpleGapPenalty took 0 sec [junit] Running org.biojava.nbio.alignment.SimpleProfilePairTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfilePairTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.183 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 sec [junit] - [junit] Testcase: testGetQuery took 0.15 sec - [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetQuery took 0.178 sec + [junit] Testcase: testGetTarget took 0.002 sec [junit] Testcase: testSimpleProfilePair took 0.009 sec [junit] Running org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleProfileProfileAlignerTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.155 sec - [junit] Testcase: testGetGapPenalty took 0.008 sec - [junit] Testcase: testGetComputationTime took 0.006 sec - [junit] Testcase: testGetQuery took 0.006 sec - [junit] Testcase: testGetScore took 0.007 sec - [junit] Testcase: testGetScoreMatrix took 0.011 sec - [junit] Testcase: testGetPair took 0.011 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.178 sec + [junit] Testcase: testGetGapPenalty took 0.01 sec + [junit] Testcase: testGetComputationTime took 0.009 sec + [junit] Testcase: testGetQuery took 0.008 sec + [junit] Testcase: testGetScore took 0.009 sec + [junit] Testcase: testGetScoreMatrix took 0.012 sec + [junit] Testcase: testGetPair took 0.012 sec [junit] Testcase: testGetProfile took 0.006 sec - [junit] Testcase: testGetMinScore took 0.003 sec + [junit] Testcase: testGetMinScore took 0.004 sec [junit] Testcase: testIsStoringScoreMatrix took 0.004 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.055 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.003 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.004 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.073 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.004 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.005 sec [junit] Testcase: testGetTarget took 0.004 sec - [junit] Testcase: testGetMaxScore took 0.003 sec + [junit] Testcase: testGetMaxScore took 0.004 sec [junit] Running org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest [junit] Testsuite: org.biojava.nbio.alignment.SimpleSubstitutionMatrixTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.181 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.215 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.215 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.013 sec - [junit] Testcase: testSetDescription took 0.029 sec - [junit] Testcase: testToString took 0.051 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.015 sec + [junit] Testcase: testSetDescription took 0.035 sec + [junit] Testcase: testToString took 0.059 sec [junit] Testcase: testCaseEquivalence took 0.002 sec - [junit] Testcase: test took 0.019 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.021 sec + [junit] Testcase: test took 0.02 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.027 sec [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.005 sec - [junit] Testcase: testSetName took 0.013 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.003 sec + [junit] Testcase: testSetName took 0.017 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.005 sec [junit] Running org.biojava.nbio.alignment.SmithWatermanTest [junit] Testsuite: org.biojava.nbio.alignment.SmithWatermanTest - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.274 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.333 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.097 sec - [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.047 sec - [junit] Testcase: testGetQuery took 0.001 sec - [junit] Testcase: testGetScore took 0.004 sec - [junit] Testcase: testGetScoreMatrix took 0.003 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.118 sec + [junit] Testcase: testGetGapPenalty took 0.002 sec + [junit] Testcase: testGetComputationTime took 0.055 sec + [junit] Testcase: testGetQuery took 0.002 sec + [junit] Testcase: testGetScore took 0.005 sec + [junit] Testcase: testGetScoreMatrix took 0.005 sec [junit] Testcase: testGetPair took 0.011 sec [junit] Testcase: testSmithWaterman took 0.003 sec [junit] Testcase: testGetProfile took 0.004 sec - [junit] Testcase: testGetMinScore took 0.002 sec - [junit] Testcase: testIsStoringScoreMatrix took 0 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.057 sec - [junit] Testcase: testSetStoringScoreMatrix took 0.011 sec + [junit] Testcase: testGetMinScore took 0.003 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.074 sec + [junit] Testcase: testSetStoringScoreMatrix took 0.013 sec [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Running org.biojava.nbio.alignment.routines.AlignerHelperTest [junit] Testsuite: org.biojava.nbio.alignment.routines.AlignerHelperTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.009 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.011 sec [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size took 0.004 sec - [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0.001 sec + [junit] Testcase: getSubproblems_should_return_score_indicies_of_alignment_subproblems took 0 sec [junit] Testcase: getSubproblems_should_allow_adjacent_anchors took 0 sec [junit] Testcase: getCuts_should_return_all_positions_when_cuts_exceeds_query_size took 0 sec - [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0.001 sec + [junit] Testcase: getSubproblems_should_allow_zero_anchors took 0 sec [junit] Testcase: getCuts_should_not_return_start_position_for_starting_anchor took 0 sec [junit] Testcase: getSubproblems_should_allow_start_and_end_anchors took 0 sec [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.248 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.283 sec [junit] - [junit] Testcase: testGetComputationTime took 0.14 sec - [junit] Testcase: testGuanUberbacher took 0.002 sec + [junit] Testcase: testGetComputationTime took 0.163 sec + [junit] Testcase: testGuanUberbacher took 0.001 sec [junit] Testcase: testGetScore took 0.001 sec - [junit] Testcase: testGetPair took 0.009 sec + [junit] Testcase: testGetPair took 0.008 sec [junit] Testcase: testGetProfile took 0.002 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_shorter_target took 0.061 sec - [junit] Testcase: should_align_multiple_cuts took 0.003 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: should_align_shorter_target took 0.067 sec + [junit] Testcase: should_align_multiple_cuts took 0.005 sec + [junit] Testcase: testGetMaxScore took 0.001 sec [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL -Total time: 22 seconds +Total time: 24 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -2616,8 +2683,8 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.aaproperties.CommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.CommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.228 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.228 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.353 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.353 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -2625,41 +2692,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 1.075 sec - [junit] Testcase: testExample1 took 0.052 sec - [junit] Testcase: testExample2 took 0.021 sec - [junit] Testcase: testExample3 took 0.008 sec - [junit] Testcase: testExample1WithCSV took 0.04 sec - [junit] Testcase: testWithCases took 0.007 sec + [junit] Testcase: testAdvancedXMLExample took 1.146 sec + [junit] Testcase: testExample1 took 0.07 sec + [junit] Testcase: testExample2 took 0.027 sec + [junit] Testcase: testExample3 took 0.011 sec + [junit] Testcase: testExample1WithCSV took 0.061 sec + [junit] Testcase: testWithCases took 0.01 sec [junit] Running org.biojava.nbio.aaproperties.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.CookBookTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.052 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.052 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.235 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.235 sec [junit] - [junit] Testcase: shortExample1 took 0.088 sec - [junit] Testcase: shortExample2 took 0.776 sec - [junit] Testcase: shortExample3 took 0.144 sec - [junit] Testcase: shortExample4 took 0.004 sec - [junit] Testcase: shortExample5 took 0.019 sec + [junit] Testcase: shortExample1 took 0.102 sec + [junit] Testcase: shortExample2 took 0.894 sec + [junit] Testcase: shortExample3 took 0.183 sec + [junit] Testcase: shortExample4 took 0.005 sec + [junit] Testcase: shortExample5 took 0.024 sec [junit] Running org.biojava.nbio.aaproperties.GenbankCommandPromptTest [junit] Testsuite: org.biojava.nbio.aaproperties.GenbankCommandPromptTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.202 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.202 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.415 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.415 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] NP_000257 133 aa linear PRI 27-MAR-2008,15043.5262,5960.0,6585.0,9.1715 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 0.982 sec - [junit] Testcase: testExample1 took 0.063 sec - [junit] Testcase: testExample2 took 0.036 sec - [junit] Testcase: testExample3 took 0.028 sec - [junit] Testcase: testExample1WithCSV took 0.042 sec - [junit] Testcase: testWithCases took 0.027 sec + [junit] Testcase: testAdvancedXMLExample took 1.141 sec + [junit] Testcase: testExample1 took 0.08 sec + [junit] Testcase: testExample2 took 0.047 sec + [junit] Testcase: testExample3 took 0.034 sec + [junit] Testcase: testExample1WithCSV took 0.052 sec + [junit] Testcase: testWithCases took 0.034 sec [junit] Running org.biojava.nbio.aaproperties.PeptidePropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.PeptidePropertiesImplTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.758 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.758 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.212 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.212 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - '1 are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. @@ -2874,74 +2941,74 @@ [junit] [main] WARN org.biojava.nbio.aaproperties.PeptidePropertiesImpl - Valid length of sequence is 0, can't divide by 0 to calculate instability index: setting instability index value to 0.0 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAbsorbance took 0.095 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 0.902 sec - [junit] Testcase: testEnrichment took 0.032 sec - [junit] Testcase: testApliphaticIndex took 0.004 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.011 sec + [junit] Testcase: testAbsorbance took 0.114 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 1.119 sec + [junit] Testcase: testEnrichment took 0.043 sec + [junit] Testcase: testApliphaticIndex took 0.005 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.012 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.057 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.075 sec [junit] Testcase: testAbsorbanceNull took 0.001 sec [junit] Testcase: testIsoelectricPointNull took 0.001 sec - [junit] Testcase: testAverageHydropathy took 0.001 sec - [junit] Testcase: testExtinctionCoefficient took 0.002 sec + [junit] Testcase: testAverageHydropathy took 0.002 sec + [junit] Testcase: testExtinctionCoefficient took 0.003 sec [junit] Testcase: testAAComposition took 0.002 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.11 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.148 sec [junit] Testcase: testMolecularWeight took 0.002 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.013 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.017 sec [junit] Testcase: testNetChargeNull took 0.002 sec [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec - [junit] Testcase: testNetCharge took 0.262 sec + [junit] Testcase: testNetCharge took 0.334 sec [junit] Testcase: testEnrichmentNull took 0.001 sec - [junit] Testcase: testInstabilityIndexNull took 0.001 sec - [junit] Testcase: testAverageHydropathyNull took 0.001 sec - [junit] Testcase: testMolecularWeightXML took 0.227 sec - [junit] Testcase: testInstabilityIndex took 0.001 sec + [junit] Testcase: testInstabilityIndexNull took 0 sec + [junit] Testcase: testAverageHydropathyNull took 0 sec + [junit] Testcase: testMolecularWeightXML took 0.292 sec + [junit] Testcase: testInstabilityIndex took 0.002 sec [junit] Running org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest [junit] Testsuite: org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec [junit] - [junit] Testcase: testFake took 0.005 sec + [junit] Testcase: testFake took 0.007 sec [junit] Running org.biojava.nbio.aaproperties.profeat.CookBookTest [junit] Testsuite: org.biojava.nbio.aaproperties.profeat.CookBookTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec [junit] - [junit] Testcase: testFakeTest took 0.037 sec + [junit] Testcase: testFakeTest took 0.045 sec [junit] Running org.biojava.nbio.aaproperties.xml.AminoAcidTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.AminoAcidTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.258 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.258 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.489 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.489 sec [junit] ------------- Standard Error ----------------- [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - 'J are being replaced with '-' [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - There exists invalid characters in the sequence. Computed results might not be precise. [junit] [main] WARN org.biojava.nbio.aaproperties.Utils - To remove this warning: Please use org.biojava.nbio.aaproperties.Utils.cleanSequence to clean sequence. [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: generateSchema took 0.689 sec - [junit] Testcase: readWithIDXml took 0.227 sec - [junit] Testcase: readMinXml took 0.086 sec - [junit] Testcase: readAdvancedXml took 0.053 sec - [junit] Testcase: generateXml took 0.045 sec - [junit] Testcase: readXml took 0.136 sec + [junit] Testcase: generateSchema took 0.81 sec + [junit] Testcase: readWithIDXml took 0.264 sec + [junit] Testcase: readMinXml took 0.113 sec + [junit] Testcase: readAdvancedXml took 0.063 sec + [junit] Testcase: generateXml took 0.051 sec + [junit] Testcase: readXml took 0.16 sec [junit] Running org.biojava.nbio.aaproperties.xml.ElementTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.ElementTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.104 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.104 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.343 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.343 sec [junit] - [junit] Testcase: generateSchema took 0.721 sec - [junit] Testcase: generateXml took 0.106 sec - [junit] Testcase: readXml took 0.256 sec + [junit] Testcase: generateSchema took 0.869 sec + [junit] Testcase: generateXml took 0.131 sec + [junit] Testcase: readXml took 0.318 sec [junit] Running org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest [junit] Testsuite: org.biojava.nbio.aaproperties.xml.GenerateJavaCodesFromTextTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 sec [junit] - [junit] Testcase: testFake took 0.037 sec + [junit] Testcase: testFake took 0.046 sec BUILD SUCCESSFUL -Total time: 23 seconds +Total time: 27 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -2958,7 +3025,7 @@ [echo] Using java version 11.0.12 BUILD SUCCESSFUL -Total time: 4 seconds +Total time: 5 seconds # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -2974,22 +3041,22 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.sequencing.io.fastq.ConvertTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.ConvertTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.266 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec [junit] - [junit] Testcase: testConvert took 0.239 sec + [junit] Testcase: testConvert took 0.247 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqBuilderTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.008 sec + [junit] Testcase: testBuildAppendSequence took 0.01 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec - [junit] Testcase: testBuild took 0.002 sec + [junit] Testcase: testBuild took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec - [junit] Testcase: testBuildDefaultVariant took 0 sec - [junit] Testcase: testBuildMissingQuality took 0 sec + [junit] Testcase: testBuildDefaultVariant took 0.001 sec + [junit] Testcase: testBuildMissingQuality took 0.001 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec @@ -2997,8 +3064,8 @@ [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0 sec - [junit] Testcase: testBuildMissingDescription took 0 sec - [junit] Testcase: testBuildNullVariant took 0.001 sec + [junit] Testcase: testBuildMissingDescription took 0.001 sec + [junit] Testcase: testBuildNullVariant took 0 sec [junit] Testcase: testBuildDefault took 0 sec [junit] Testcase: testBuildMissingSequence took 0 sec [junit] Testcase: testBuildNullQuality took 0 sec @@ -3006,194 +3073,194 @@ [junit] Testcase: testConstructor took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] [junit] Testcase: testImmutable took 0.004 sec - [junit] Testcase: testBuilder took 0.005 sec + [junit] Testcase: testBuilder took 0.006 sec [junit] Testcase: testVariant took 0 sec - [junit] Testcase: testQuality took 0.003 sec + [junit] Testcase: testQuality took 0.005 sec [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0.001 sec [junit] Testcase: testDescription took 0 sec - [junit] Testcase: testConstructor took 0.001 sec + [junit] Testcase: testConstructor took 0 sec [junit] Testcase: testSequence took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqToolsTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqToolsTest - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.192 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.004 sec - [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.002 sec - [junit] Testcase: testConvertNullVariant took 0 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.005 sec + [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.004 sec + [junit] Testcase: testConvertNullVariant took 0.001 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.002 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.093 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.111 sec [junit] Testcase: testQualityScoresIntArrayNullFastq took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0 sec [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0 sec [junit] Testcase: testQualityScoresNullIntArray took 0 sec - [junit] Testcase: testConvertNullFastq took 0 sec + [junit] Testcase: testConvertNullFastq took 0.001 sec [junit] Testcase: testConvertQualitiesSameVariant took 0 sec [junit] Testcase: testCreateQualityScores took 0.001 sec [junit] Testcase: testCreateErrorProbabilities took 0 sec [junit] Testcase: testCreateDNASequenceNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec + [junit] Testcase: testConvertQualitiesNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0.001 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0.001 sec - [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec + [junit] Testcase: testConvertQualitiesSangerToSolexa took 0.001 sec [junit] Testcase: testConvertQualitiesSolexaToIllumina took 0 sec - [junit] Testcase: testConvertQualitiesSangerToIllumina took 0.001 sec + [junit] Testcase: testConvertQualitiesSangerToIllumina took 0 sec [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec - [junit] Testcase: testQualityScoresNullFastq took 0 sec - [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec + [junit] Testcase: testQualityScoresNullFastq took 0.001 sec + [junit] Testcase: testConvertQualitiesSolexaToSanger took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec [junit] Testcase: testToListNotAList took 0.003 sec - [junit] Testcase: testConvertQualitiesNullVariant took 0.001 sec + [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec - [junit] Testcase: testQualityScores took 0.007 sec - [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec + [junit] Testcase: testQualityScores took 0.009 sec + [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0.001 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0 sec [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq took 0 sec [junit] Testcase: testCreateDNASequence took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilities took 0.001 sec [junit] Testcase: testCreateDNASequenceWithQualityScores took 0.001 sec - [junit] Testcase: testQualityScoresIntArray took 0 sec + [junit] Testcase: testQualityScoresIntArray took 0.001 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec [junit] Testcase: testToList took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilities took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec [junit] [junit] Testcase: testParseFastqVariant took 0.007 sec [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec - [junit] Testcase: testIsSanger took 0.004 sec - [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec - [junit] Testcase: testIsSolexa took 0 sec + [junit] Testcase: testIsSanger took 0.005 sec + [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 sec + [junit] Testcase: testIsSolexa took 0.001 sec [junit] Testcase: testIsIllumina took 0 sec [junit] Testcase: testDescription took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.31 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.065 sec - [junit] Testcase: testWrappingAsIllumina took 0.006 sec - [junit] Testcase: testValidateDescription took 0.016 sec - [junit] Testcase: testValidateRepeatDescription took 0.006 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.004 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.005 sec - [junit] Testcase: testLongReadsAsIllumina took 0.007 sec - [junit] Testcase: testParseNullReadable took 0.002 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.042 sec + [junit] Testcase: testFullRangeAsIllumina took 0.078 sec + [junit] Testcase: testWrappingAsIllumina took 0.008 sec + [junit] Testcase: testValidateDescription took 0.019 sec + [junit] Testcase: testValidateRepeatDescription took 0.007 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.006 sec + [junit] Testcase: testMiscRnaAsIllumina took 0.007 sec + [junit] Testcase: testLongReadsAsIllumina took 0.008 sec + [junit] Testcase: testParseNullReadable took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.046 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.061 sec + [junit] Testcase: testErrorExamples took 0.07 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0.001 sec [junit] Testcase: testReadInputStream took 0 sec [junit] Testcase: testWrappedSequence took 0.003 sec [junit] Testcase: testReadEmptyInputStream took 0.003 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0 sec + [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testReadFile took 0.001 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec - [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0 sec + [junit] Testcase: testCreateFastqReader took 0.001 sec + [junit] Testcase: testReadURL took 0.002 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0.002 sec + [junit] Testcase: testWrappedQuality took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.014 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.018 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.036 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec + [junit] Testcase: testWriteFileIterable took 0.042 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testWriteFileVararg took 0.004 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqReaderTest - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.288 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.331 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.331 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.065 sec - [junit] Testcase: testFullRangeAsSanger took 0.006 sec - [junit] Testcase: testWrappingOriginal took 0.006 sec - [junit] Testcase: testLongReadsOriginal took 0.01 sec + [junit] Testcase: testMiscRnaAsSanger took 0.077 sec + [junit] Testcase: testFullRangeAsSanger took 0.007 sec + [junit] Testcase: testWrappingOriginal took 0.008 sec + [junit] Testcase: testLongReadsOriginal took 0.013 sec [junit] Testcase: testMiscDnaOriginal took 0.005 sec - [junit] Testcase: testMiscRnaOriginal took 0.005 sec - [junit] Testcase: testValidateDescription took 0.016 sec - [junit] Testcase: testValidateRepeatDescription took 0.004 sec - [junit] Testcase: testFullRangeOriginal took 0.004 sec + [junit] Testcase: testMiscRnaOriginal took 0.006 sec + [junit] Testcase: testValidateDescription took 0.019 sec + [junit] Testcase: testValidateRepeatDescription took 0.003 sec + [junit] Testcase: testFullRangeOriginal took 0.003 sec [junit] Testcase: testWrappingAsSanger took 0.004 sec [junit] Testcase: testLongReadsAsSanger took 0.006 sec - [junit] Testcase: testMiscDnaAsSanger took 0.003 sec + [junit] Testcase: testMiscDnaAsSanger took 0.004 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.04 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.043 sec [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.058 sec + [junit] Testcase: testErrorExamples took 0.067 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.002 sec + [junit] Testcase: testWrappedSequence took 0.003 sec [junit] Testcase: testReadEmptyInputStream took 0.002 sec [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0 sec - [junit] Testcase: testCreateFastqWriter took 0 sec + [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec [junit] Testcase: testReadEmptyURL took 0.001 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec [junit] Testcase: testWrappedQuality took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.103 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.015 sec + [junit] Testcase: testConvertNotSangerVariant took 0.018 sec [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.036 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec + [junit] Testcase: testWriteFileIterable took 0.041 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0 sec - [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testAppendIterable took 0.001 sec + [junit] Testcase: testCreateFastqWriter took 0.001 sec + [junit] Testcase: testWriteFileVararg took 0.004 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqReaderTest - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.265 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.307 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.065 sec - [junit] Testcase: testFullRangeAsSolexa took 0.005 sec - [junit] Testcase: testValidateDescription took 0.016 sec - [junit] Testcase: testValidateRepeatDescription took 0.006 sec - [junit] Testcase: testWrappingAsSolexa took 0.005 sec - [junit] Testcase: testLongReadsAsSolexa took 0.008 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.003 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.078 sec + [junit] Testcase: testFullRangeAsSolexa took 0.007 sec + [junit] Testcase: testValidateDescription took 0.02 sec + [junit] Testcase: testValidateRepeatDescription took 0.007 sec + [junit] Testcase: testWrappingAsSolexa took 0.006 sec + [junit] Testcase: testLongReadsAsSolexa took 0.01 sec + [junit] Testcase: testMiscDnaAsSolexa took 0.004 sec [junit] Testcase: testParseNullReadable took 0.002 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.043 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.045 sec [junit] Testcase: testReadEmptyFile took 0 sec - [junit] Testcase: testErrorExamples took 0.059 sec + [junit] Testcase: testErrorExamples took 0.069 sec [junit] Testcase: testParse took 0.002 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testReadInputStream took 0 sec + [junit] Testcase: testReadInputStream took 0.001 sec [junit] Testcase: testWrappedSequence took 0.003 sec - [junit] Testcase: testReadEmptyInputStream took 0.003 sec + [junit] Testcase: testReadEmptyInputStream took 0.002 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0 sec + [junit] Testcase: testReadFile took 0.001 sec [junit] Testcase: testMultipleWrappedQuality took 0.003 sec - [junit] Testcase: testCreateFastqReader took 0 sec + [junit] Testcase: testCreateFastqReader took 0.001 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec [junit] Testcase: testReadEmptyURL took 0.001 sec @@ -3201,29 +3268,29 @@ [junit] Testcase: testWrappedQuality took 0.003 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.015 sec - [junit] Testcase: testAppendVararg took 0 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.018 sec + [junit] Testcase: testAppendVararg took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.004 sec - [junit] Testcase: testWriteFileIterable took 0.036 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.005 sec + [junit] Testcase: testWriteFileIterable took 0.044 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.003 sec + [junit] Testcase: testWriteFileVararg took 0.004 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.StreamingFastqParserTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] - [junit] Testcase: testStreamNullVariant took 0.004 sec - [junit] Testcase: testStreamNullListener took 0.005 sec - [junit] Testcase: testStreamNullReadable took 0.002 sec + [junit] Testcase: testStreamNullVariant took 0.006 sec + [junit] Testcase: testStreamNullListener took 0.006 sec + [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL -Total time: 18 seconds +Total time: 20 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -3244,39 +3311,39 @@ [echo] Using java version 11.0.12 [junit] Running org.biojava.nbio.structure.gui.JmolViewerImplTest [junit] Testsuite: org.biojava.nbio.structure.gui.JmolViewerImplTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec [junit] [junit] Testcase: testMe took 0.002 sec [junit] Running org.biojava.nbio.structure.gui.RenderStyleTest [junit] Testsuite: org.biojava.nbio.structure.gui.RenderStyleTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] - [junit] Testcase: testSomeMethod took 0.002 sec + [junit] Testcase: testSomeMethod took 0.001 sec [junit] Running org.biojava.nbio.structure.gui.StructureViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.StructureViewerTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec [junit] [junit] Testcase: testGetColor took 0.005 sec [junit] Testcase: testSetStructure took 0 sec [junit] Testcase: testClear took 0 sec [junit] Testcase: testGetSelection took 0.004 sec - [junit] Testcase: testRepaint took 0.001 sec - [junit] Testcase: testSetSelection took 0 sec + [junit] Testcase: testRepaint took 0 sec + [junit] Testcase: testSetSelection took 0.001 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 9 seconds cd biojava-ontology && ant test Buildfile: /build/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -3291,8 +3358,8 @@ [echo] Using java version 11.0.12 BUILD SUCCESSFUL -Total time: 4 seconds -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +Total time: 5 seconds +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dpkg: warning: --compare-versions used with obsolete relation operator '>' @@ -3301,8 +3368,8 @@ dh_prep dh_install debian/rules override_jh_installjavadoc -make[1]: Entering directory '/build/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +make[1]: ingresso nella directory «/build/biojava4-live-4.2.12+dfsg» +dpkg: attenzione: --compare-versions utilizzato con l'operatore di relazione obsoleto ">" jh_installjavadoc rdfind -makesymlinks true -followsymlinks true \ $(dpkg -L $(apt-cache show default-jdk-doc | grep Depends | awk '{print $2}') | grep /usr/share/doc/ | head -n1) \ @@ -3323,7 +3390,7 @@ Failed moving /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to a temporary file Failed to make symlink /usr/share/doc/openjdk-11-doc/api/jquery/external/jquery/jquery.js to /usr/share/doc/openjdk-11-doc/api/jquery/jquery-3.5.1.js Making 19 links. -make[1]: Leaving directory '/build/biojava4-live-4.2.12+dfsg' +make[1]: uscita dalla directory «/build/biojava4-live-4.2.12+dfsg» dh_installdocs dh_installchangelogs dh_lintian @@ -3341,9 +3408,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbiojava4-java' in '../libbiojava4-java_4.2.12+dfsg-3.1_all.deb'. -dpkg-deb: building package 'libbiojava4-java-doc' in '../libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb'. -dpkg-deb: building package 'libbiojava4.0-java' in '../libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb'. +dpkg-deb: generazione del pacchetto "libbiojava4.0-java" in "../libbiojava4.0-java_4.2.12+dfsg-3.1_all.deb". +dpkg-deb: generazione del pacchetto "libbiojava4-java" in "../libbiojava4-java_4.2.12+dfsg-3.1_all.deb". +dpkg-deb: generazione del pacchetto "libbiojava4-java-doc" in "../libbiojava4-java-doc_4.2.12+dfsg-3.1_all.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava4-live_4.2.12+dfsg-3.1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3351,12 +3418,14 @@ 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/2657/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2657/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/21715 and its subdirectories -I: Current time: Fri Aug 13 10:48:09 -12 2021 -I: pbuilder-time-stamp: 1628894889 +I: removing directory /srv/workspace/pbuilder/2657 and its subdirectories +I: Current time: Sat Aug 14 12:59:58 +14 2021 +I: pbuilder-time-stamp: 1628895598