Diff of the two buildlogs: -- --- b1/build.log 2024-08-07 19:39:41.925733186 +0000 +++ b2/build.log 2024-08-07 19:43:37.559727575 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 7 07:12:13 -12 2024 -I: pbuilder-time-stamp: 1723057933 +I: Current time: Wed Sep 10 16:02:44 +14 2025 +I: pbuilder-time-stamp: 1757469764 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ 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.ja8_ZKF2/trustedkeys.kbx': General error -gpgv: Signature made Mon Jul 13 07:29:24 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.sd2Tl3A8/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 @@ -36,135 +36,166 @@ dpkg-source: info: applying ignore_fake_tests I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/400204/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 10 16:02 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=42 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0d84b0ff14cd4308a86b210f5525b20c' - 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='400204' - PS1='# ' - PS2='> ' + INVOCATION_ID=99091d474dc946b891e8ffe869d4ded3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=522086 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Effg9iaO/pbuilderrc_7DLH --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Effg9iaO/b1 --logfile b1/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Effg9iaO/pbuilderrc_1bhp --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Effg9iaO/b2 --logfile b2/build.log biojava4-live_4.2.12+dfsg-3.1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.9.7+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1~bpo12+1 (2024-07-03) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Mar 27 22:09 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Mar 27 22:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Mar 27 22:09 more - -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount - -rwxr-xr-x 1 root root 18664 Mar 27 22:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 6 21:26 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Mar 27 22:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Mar 27 22:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 22:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/400204/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Mar 29 2024 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 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 2024 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Mar 29 2024 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Mar 29 2024 more + -rwsr-xr-x 1 root root 55528 Mar 29 2024 mount + -rwxr-xr-x 1 root root 18664 Mar 29 2024 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Sep 10 16:02 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Mar 29 2024 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 2024 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Mar 29 2024 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 2024 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -479,7 +510,7 @@ Get: 219 http://deb.debian.org/debian bullseye/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libxmlunit-java all 1.6-2 [100 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 rdfind amd64 1.4.1-1+b3 [40.7 kB] -Fetched 208 MB in 10s (20.6 MB/s) +Fetched 208 MB in 5s (40.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19711 files and directories currently installed.) @@ -1401,135 +1432,135 @@ Setting up javahelper (0.78) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:GTS_Root_R1.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:emSign_Root_CA_-_C1.pem -Adding debian:Security_Communication_RootCA2.pem -Adding debian:Hongkong_Post_Root_CA_3.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:Amazon_Root_CA_2.pem Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:Amazon_Root_CA_1.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:Certigna.pem -Adding debian:Secure_Global_CA.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Amazon_Root_CA_3.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:NAVER_Global_Root_Certification_Authority.pem +Adding debian:Izenpe.com.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:UCA_Extended_Validation_Root.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:Entrust_Root_Certification_Authority_-_G4.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:GTS_Root_R3.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:Secure_Global_CA.pem Adding debian:CFCA_EV_ROOT.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:emSign_ECC_Root_CA_-_G3.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:ISRG_Root_X1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:emSign_ECC_Root_CA_-_C3.pem +Adding debian:emSign_Root_CA_-_C1.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:SecureTrust_CA.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem +Adding debian:Security_Communication_Root_CA.pem Adding debian:SecureSign_RootCA11.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:DigiCert_Trusted_Root_G4.pem -Adding debian:Izenpe.com.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem -Adding debian:NAVER_Global_Root_Certification_Authority.pem -Adding debian:EC-ACC.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:GTS_Root_R2.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:UCA_Global_G2_Root.pem -Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:GTS_Root_R4.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:Entrust_Root_Certification_Authority_-_G4.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:emSign_Root_CA_-_G1.pem -Adding debian:UCA_Extended_Validation_Root.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:Certigna_Root_CA.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:GTS_Root_R4.pem -Adding debian:AffirmTrust_Premium.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:GTS_Root_R2.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:certSIGN_Root_CA_G2.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Security_Communication_RootCA2.pem Adding debian:Starfield_Class_2_CA.pem -Adding debian:e-Szigno_Root_CA_2017.pem -Adding debian:SecureTrust_CA.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:XRamp_Global_CA_Root.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:certSIGN_Root_CA_G2.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:TrustCor_ECA-1.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:emSign_Root_CA_-_G1.pem +Adding debian:Certigna_Root_CA.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:GTS_Root_R1.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:GTS_Root_R3.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem +Adding debian:Hongkong_Post_Root_CA_3.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:EC-ACC.pem Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:e-Szigno_Root_CA_2017.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem done. Setting up junit4 (4.13.1-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... @@ -1561,7 +1592,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/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 +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/522086/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -1574,7 +1609,7 @@ jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' dh_clean rm -rf build rm -rf dist @@ -1595,7 +1630,7 @@ dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' 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 @@ -1617,7 +1652,7 @@ jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' 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,' \ @@ -1639,7 +1674,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-jcolorbrewer.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 1 second cd biojava-forester && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-forester/build.xml @@ -1655,7 +1690,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-forester.jar BUILD SUCCESSFUL -Total time: 54 seconds +Total time: 5 seconds cd biojava-core && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml @@ -1673,7 +1708,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-core.jar BUILD SUCCESSFUL -Total time: 24 seconds +Total time: 3 seconds cd biojava-phylo && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-phylo/build.xml @@ -1687,7 +1722,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-phylo.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 1 second cd biojava-alignment && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -1703,7 +1738,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-alignment.jar BUILD SUCCESSFUL -Total time: 11 seconds +Total time: 1 second cd biojava-aa-prop && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -1721,7 +1756,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-aa-prop.jar BUILD SUCCESSFUL -Total time: 9 seconds +Total time: 1 second cd biojava-genome && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-genome/build.xml @@ -1737,7 +1772,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-genome.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 1 second cd biojava-sequencing && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -1752,7 +1787,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-sequencing.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 1 second cd biojava-structure && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure/build.xml @@ -1770,7 +1805,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-structure.jar BUILD SUCCESSFUL -Total time: 53 seconds +Total time: 6 seconds cd biojava-structure-gui && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-structure-gui/build.xml @@ -1788,7 +1823,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-structure-gui.jar BUILD SUCCESSFUL -Total time: 33 seconds +Total time: 3 seconds cd biojava-modfinder && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-modfinder/build.xml @@ -1804,7 +1839,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-modfinder.jar BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 1 second cd biojava-ontology && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -1822,7 +1857,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-ontology.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 1 second cd biojava-protein-disorder && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-disorder/build.xml @@ -1838,7 +1873,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-disorder.jar BUILD SUCCESSFUL -Total time: 11 seconds +Total time: 1 second cd biojava-protein-comparison-tool && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-protein-comparison-tool/build.xml @@ -1852,7 +1887,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-protein-comparison-tool.jar BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 0 seconds cd biojava-ws && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ws/build.xml @@ -1866,7 +1901,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-ws.jar BUILD SUCCESSFUL -Total time: 10 seconds +Total time: 1 second cd biojava-survival && ant jar Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-survival/build.xml @@ -1880,7 +1915,7 @@ [jar] Building jar: /build/reproducible-path/biojava4-live-4.2.12+dfsg/dist/biojava4-survival.jar BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 2 seconds # make doc rm -rf biojavadoc mkdir biojavadoc @@ -2173,12 +2208,12 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 1 minute 31 seconds +Total time: 13 seconds # rm -rf biojavadoc make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' echo '*********************************************************************************' ********************************************************************************* echo '* The following test is ignored since under certain circumstances it might fail *' @@ -2209,169 +2244,169 @@ [echo] Using java version 11.0.23 [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: 0.602 sec - [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.602 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 sec + [junit] Tests run: 33, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.048 sec [junit] - [junit] Testcase: testGetIndexOf took 0.083 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetIndexOf took 0.017 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds took 0 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds2 took 0 sec [junit] Testcase: testGetSequenceIndexAtOutOfBounds3 took 0 sec - [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetSequenceIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetNumGaps took 0.001 sec [junit] Testcase: testGetStart took 0 sec - [junit] Testcase: testGetSequenceIndexAt took 0.006 sec + [junit] Testcase: testGetSequenceIndexAt took 0 sec [junit] Testcase: testGetAccession took 0.001 sec - [junit] Testcase: testToString took 0.011 sec - [junit] Testcase: testSimpleAlignedSequenceLong took 0.002 sec - [junit] Testcase: testCountCompounds took 0.007 sec + [junit] Testcase: testToString took 0.001 sec + [junit] Testcase: testSimpleAlignedSequenceLong took 0 sec + [junit] Testcase: testCountCompounds took 0 sec [junit] Testcase: testGetAlignmentIndexAt took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.011 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.009 sec - [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0.011 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds took 0 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds3 took 0.002 sec + [junit] Testcase: testGetAlignmentIndexAtOutOfBounds4 took 0 sec [junit] Testcase: testGetSubSequence took 0 sec [junit] SKIPPED - [junit] Testcase: testGetAsList took 0.014 sec - [junit] Testcase: testGetOriginalSequence took 0.001 sec + [junit] Testcase: testGetAsList took 0.001 sec + [junit] Testcase: testGetOriginalSequence took 0 sec [junit] Testcase: testGetCompoundAt took 0.001 sec [junit] Testcase: testGetLength took 0 sec - [junit] Testcase: testIsCircular took 0.001 sec - [junit] Testcase: testGetEnd took 0.001 sec - [junit] Testcase: testSimpleAlignedSequenceLocal took 0.005 sec - [junit] Testcase: testSimpleAlignedSequenceShort took 0.001 sec - [junit] Testcase: testGetOverlapCount took 0.001 sec - [junit] Testcase: testGetCompoundSet took 0.001 sec - [junit] Testcase: testGetLocationInAlignment took 0.002 sec + [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetEnd took 0 sec + [junit] Testcase: testSimpleAlignedSequenceLocal took 0 sec + [junit] Testcase: testSimpleAlignedSequenceShort took 0 sec + [junit] Testcase: testGetOverlapCount took 0 sec + [junit] Testcase: testGetCompoundSet took 0 sec + [junit] Testcase: testGetLocationInAlignment took 0 sec [junit] Testcase: testIterator took 0.001 sec - [junit] Testcase: testGetSequenceAsString took 0.001 sec - [junit] Testcase: testGetLastIndexOf took 0.001 sec - [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.019 sec + [junit] Testcase: testGetSequenceAsString took 0 sec + [junit] Testcase: testGetLastIndexOf took 0 sec + [junit] Testcase: testGetSequenceAsStringIntegerIntegerStrand took 0.002 sec [junit] Running org.biojava.nbio.core.alignment.SimpleProfileTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleProfileTest - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1 sec - [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 1 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.09 sec + [junit] Tests run: 54, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0.09 sec [junit] - [junit] Testcase: testGetIndexOf took 0.196 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.011 sec - [junit] Testcase: testGetAlignedSequenceInt took 0.003 sec - [junit] Testcase: testToStringInt took 0.034 sec - [junit] Testcase: testToString took 0.002 sec - [junit] Testcase: testToStringFormatted took 0.068 sec + [junit] Testcase: testGetIndexOf took 0.031 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds took 0.001 sec + [junit] Testcase: testGetAlignedSequenceInt took 0.001 sec + [junit] Testcase: testToStringInt took 0.005 sec + [junit] Testcase: testToString took 0 sec + [junit] Testcase: testToStringFormatted took 0.011 sec [junit] Testcase: testSimpleProfile took 0.001 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 0.001 sec + [junit] Testcase: testGetSize took 0 sec + [junit] Testcase: testGetAlignedSequenceS took 0 sec + [junit] Testcase: testGetAlignedSequences took 0.001 sec + [junit] Testcase: testGetOriginalSequences took 0 sec [junit] Testcase: testGetSubProfile took 0 sec [junit] SKIPPED - [junit] Testcase: testGetCompoundAtSInt took 0.002 sec - [junit] Testcase: testGetAlignedSequencesSArray took 0.002 sec - [junit] Testcase: testGetIndicesAt took 0.01 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0.002 sec - [junit] Testcase: testGetAlignedSequencesIntArray took 0.009 sec - [junit] Testcase: testGetCompoundAtIntInt took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0.007 sec - [junit] Testcase: testGetLength took 0.004 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds took 0.001 sec - [junit] Testcase: testIsCircular took 0.006 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0.002 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0.005 sec - [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetCompoundAtSInt took 0 sec + [junit] Testcase: testGetAlignedSequencesSArray took 0 sec + [junit] Testcase: testGetIndicesAt took 0.002 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds took 0 sec + [junit] Testcase: testGetAlignedSequencesIntArray took 0.001 sec + [junit] Testcase: testGetCompoundAtIntInt took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds took 0 sec + [junit] Testcase: testGetLength took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds took 0 sec + [junit] Testcase: testIsCircular took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds5 took 0 sec + [junit] Testcase: testGetCompoundsAtOutOfBounds6 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.002 sec - [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds4 took 0 sec + [junit] Testcase: testGetIndicesAtOutOfBounds5 took 0.001 sec + [junit] Testcase: testGetIndicesAtOutOfBounds6 took 0 sec [junit] Testcase: testGetAlignedSequenceIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.002 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0.003 sec - [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetCompoundSet took 0.001 sec - [junit] Testcase: testGetCompoundsAt took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds3 took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds5 took 0 sec + [junit] Testcase: testGetAlignedSequenceIntOutOfBounds6 took 0 sec + [junit] Testcase: testGetCompoundSet took 0 sec + [junit] Testcase: testGetCompoundsAt took 0 sec [junit] Testcase: testGetCompoundAtSIntOutOfBounds2 took 0 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0.002 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0.001 sec - [junit] Testcase: testIterator took 0.002 sec - [junit] Testcase: testGetLastIndexOf took 0.003 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0.007 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0.001 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundAtSIntOutOfBounds5 took 0 sec + [junit] Testcase: testIterator took 0.001 sec + [junit] Testcase: testGetLastIndexOf took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds4 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds5 took 0 sec [junit] Testcase: testGetCompoundAtIntIntOutOfBounds6 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0.001 sec - [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0.001 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds7 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds8 took 0 sec + [junit] Testcase: testGetCompoundAtIntIntOutOfBounds9 took 0 sec [junit] Testcase: testGetIndicesAtOutOfBounds took 0 sec [junit] Running org.biojava.nbio.core.alignment.SimpleSequencePairTest [junit] Testsuite: org.biojava.nbio.core.alignment.SimpleSequencePairTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.598 sec - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.598 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.278 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0.002 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds took 0.031 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds2 took 0 sec [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0.006 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds4 took 0 sec [junit] Testcase: testGetQuery took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0.01 sec - [junit] Testcase: testGetIndexInTargetAt took 0.006 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0.003 sec - [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInTargetForQueryAtOutOfBounds took 0 sec + [junit] Testcase: testGetIndexInTargetAt took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds3 took 0 sec [junit] Testcase: testGetIndexInQueryForTargetAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds took 0.001 sec [junit] Testcase: testGetCompoundInQueryAt took 0.001 sec [junit] Testcase: testGetIndexInQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.004 sec - [junit] Testcase: testGetIndexInQueryForTargetAt took 0.001 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetIndexInQueryAtOutOfBounds4 took 0.001 sec + [junit] Testcase: testGetIndexInQueryForTargetAt took 0 sec [junit] Testcase: testGetIndexInTargetAtOutOfBounds took 0 sec - [junit] Testcase: testGetNumIdenticals took 0.001 sec - [junit] Testcase: testGetIndexInTargetForQueryAt took 0.001 sec - [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0.001 sec + [junit] Testcase: testGetNumIdenticals took 0 sec + [junit] Testcase: testGetIndexInTargetForQueryAt took 0 sec + [junit] Testcase: testGetIndexInTargetAtOutOfBounds2 took 0 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 sec - [junit] Testcase: testGetIndexInQueryAt took 0 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0.001 sec + [junit] Testcase: testGetIndexInQueryAt took 0.001 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInQueryAtOutOfBounds3 took 0 sec [junit] Testcase: testGetCompoundInQueryAtOutOfBounds4 took 0.001 sec - [junit] Testcase: testGetTarget took 0.005 sec + [junit] Testcase: testGetTarget took 0 sec [junit] Testcase: testGetCompoundInTargetAtOutOfBounds took 0.001 sec - [junit] Testcase: testGetNumSimilars took 0.02 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0.001 sec - [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.017 sec + [junit] Testcase: testGetNumSimilars took 0 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds2 took 0 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds3 took 0 sec + [junit] Testcase: testGetCompoundInTargetAtOutOfBounds4 took 0.001 sec [junit] 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: 0.339 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.339 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] ------------- Standard Output --------------- [junit] getAlignment [junit] hashCode [junit] equals [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetAlignment took 0.303 sec - [junit] Testcase: testHashCode took 0.001 sec - [junit] Testcase: testEquals took 0.002 sec + [junit] Testcase: testGetAlignment took 0.038 sec + [junit] Testcase: testHashCode took 0 sec + [junit] Testcase: testEquals took 0 sec [junit] Running org.biojava.nbio.core.search.io.SearchIOTest [junit] Testsuite: org.biojava.nbio.core.search.io.SearchIOTest - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.714 sec - [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.714 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.17 sec + [junit] Tests run: 3, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.17 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.core.search.io.Hsp - Start reading /build/reproducible-path/biojava4-live-4.2.12+dfsg/buildtest/biojava4-core/classes/org/biojava/nbio/core/search/io/blast/testBlastReport.blastxml - [junit] Aug 07, 2024 7:27:43 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Sep 10, 2025 4:05:36 PM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects [junit] INFO: Query for hits - [junit] Aug 07, 2024 7:27:43 AM org.biojava.nbio.core.search.io.blast.BlastTabularParser createObjects + [junit] Sep 10, 2025 4:05:36 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/reproducible-path/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 0.354 sec + [junit] Testcase: testConstructorWithEvalueHspFilter took 0.103 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2382,8 +2417,8 @@ [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 0.287 sec - [junit] Testcase: testConstructorWithoutFactoryGuess took 0.011 sec + [junit] Testcase: testConstructorWithFactoryGuess took 0.054 sec + [junit] Testcase: testConstructorWithoutFactoryGuess took 0.003 sec [junit] FAILED [junit] test failed: [junit] www.ncbi.nlm.nih.gov @@ -2398,7 +2433,7 @@ BUILD FAILED /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-core/build.xml:123: Test org.biojava.nbio.core.search.io.SearchIOTest failed -Total time: 27 seconds +Total time: 4 seconds cd biojava-alignment && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-alignment/build.xml @@ -2413,32 +2448,32 @@ [echo] Using java version 11.0.23 [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: 0.227 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testGetQuery took 0.066 sec - [junit] Testcase: testGetScore took 0.024 sec + [junit] Testcase: testGetQuery took 0.029 sec + [junit] Testcase: testGetScore took 0.011 sec [junit] Testcase: testFractionalIdentityScorerPairwiseSequenceAlignerOfSC took 0 sec - [junit] Testcase: testGetMinScore took 0.007 sec - [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0.001 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testFractionalIdentityScorerSequencePairOfSC took 0 sec [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetMaxScore took 0 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: 0.323 sec - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.323 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testGetQuery took 0.112 sec - [junit] Testcase: testGetScore took 0.03 sec - [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0.002 sec - [junit] Testcase: testGetMinScore took 0.004 sec - [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0.001 sec - [junit] Testcase: testGetTarget took 0.001 sec - [junit] Testcase: testGetMaxScore took 0.004 sec + [junit] Testcase: testGetQuery took 0.03 sec + [junit] Testcase: testGetScore took 0.011 sec + [junit] Testcase: testFractionalSimilarityScorerSequencePairOfSC took 0 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testFractionalSimilarityScorerPairwiseSequenceAlignerOfSC took 0 sec + [junit] Testcase: testGetTarget took 0 sec + [junit] Testcase: testGetMaxScore took 0.001 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: 0.548 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.548 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.104 sec [junit] ------------- Standard Error ----------------- [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed @@ -2450,157 +2485,157 @@ [junit] [main] INFO org.biojava.nbio.phylo.TreeConstructor - Tree Completed [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGuideTree took 0.164 sec - [junit] Testcase: testToString took 0.004 sec - [junit] Testcase: testGetScoreMatrix took 0.006 sec - [junit] Testcase: testGetRoot took 0.034 sec - [junit] Testcase: testGetSequences took 0.003 sec - [junit] Testcase: testGetDistanceMatrix took 0.004 sec - [junit] Testcase: testGetAllPairsScores took 0.003 sec - [junit] Testcase: testIterator took 0.002 sec + [junit] Testcase: testGuideTree took 0.068 sec + [junit] Testcase: testToString took 0.002 sec + [junit] Testcase: testGetScoreMatrix took 0.003 sec + [junit] Testcase: testGetRoot took 0.014 sec + [junit] Testcase: testGetSequences took 0.001 sec + [junit] Testcase: testGetDistanceMatrix took 0.001 sec + [junit] Testcase: testGetAllPairsScores took 0.001 sec + [junit] Testcase: testIterator took 0.001 sec [junit] 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: 0.244 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 sec [junit] - [junit] Testcase: shouldAllowZeroLengthMatches took 0.091 sec + [junit] Testcase: shouldAllowZeroLengthMatches took 0.046 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: 0.714 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.714 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.328 sec [junit] ------------- Standard Output --------------- [junit] CG--TATATATCGCGCGCGCGATATATATATCT-TCTCTAAAAAAA [junit] GGTATATATATCGCGCGCACGAT-TATATATCTCTCTCTAAAAAAA [junit] [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.149 sec - [junit] Testcase: testGetGapPenalty took 0.001 sec - [junit] Testcase: testGetComputationTime took 0.051 sec - [junit] Testcase: should_align_middle_anchor took 0.063 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.028 sec + [junit] Testcase: testGetGapPenalty took 0 sec + [junit] Testcase: testGetComputationTime took 0.011 sec + [junit] Testcase: should_align_middle_anchor took 0.011 sec [junit] Testcase: testGetQuery took 0 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: testGetScore took 0.001 sec + [junit] Testcase: testNeedlemanWunsch took 0 sec + [junit] Testcase: should_align_all_anchored took 0 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 0.004 sec - [junit] Testcase: testGetProfile took 0.006 sec - [junit] Testcase: testGetMinScore took 0 sec - [junit] Testcase: should_align_ending_anchor took 0.001 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.003 sec - [junit] Testcase: testComplex took 0.022 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.033 sec + [junit] Testcase: testGetPair took 0.001 sec + [junit] Testcase: should_align_multiple_anchors took 0 sec + [junit] Testcase: testAnchoredDNAAlignment took 0.001 sec + [junit] Testcase: testGetProfile took 0.001 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: should_align_ending_anchor took 0 sec + [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec + [junit] Testcase: testComplex took 0.005 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.008 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: testGetMaxScore took 0.001 sec - [junit] Testcase: testIntOverflowBug took 0.273 sec + [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: testIntOverflowBug took 0.079 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: 0.05 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] - [junit] Testcase: testOpenPenalty took 0.008 sec - [junit] Testcase: testType took 0.001 sec - [junit] Testcase: testExtensionPenalty took 0 sec + [junit] Testcase: testOpenPenalty took 0.002 sec + [junit] Testcase: testType took 0 sec + [junit] Testcase: testExtensionPenalty took 0.001 sec [junit] Testcase: testSimpleGapPenaltyShortShort took 0 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: 0.282 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.282 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testGetQuery took 0.225 sec - [junit] Testcase: testGetTarget took 0.003 sec - [junit] Testcase: testSimpleProfilePair took 0.011 sec + [junit] Testcase: testGetQuery took 0.041 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testSimpleProfilePair took 0.002 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: 0.443 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.443 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.075 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.256 sec - [junit] Testcase: testGetGapPenalty took 0.015 sec - [junit] Testcase: testGetComputationTime took 0.004 sec - [junit] Testcase: testGetQuery took 0.01 sec - [junit] Testcase: testGetScore took 0.002 sec - [junit] Testcase: testGetScoreMatrix took 0.007 sec - [junit] Testcase: testGetPair took 0.019 sec - [junit] Testcase: testGetProfile took 0.003 sec - [junit] Testcase: testGetMinScore took 0.007 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.002 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.046 sec - [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.002 sec - [junit] Testcase: testSimpleProfileProfileAligner took 0.014 sec - [junit] Testcase: testGetTarget took 0.01 sec - [junit] Testcase: testGetMaxScore took 0.002 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.04 sec + [junit] Testcase: testGetGapPenalty took 0.002 sec + [junit] Testcase: testGetComputationTime took 0.001 sec + [junit] Testcase: testGetQuery took 0.001 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: testGetProfile took 0.001 sec + [junit] Testcase: testGetMinScore took 0.001 sec + [junit] Testcase: testIsStoringScoreMatrix took 0 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.011 sec + [junit] Testcase: testSimpleProfileProfileAlignerProfileOfSCProfileOfSCGapPenaltySubstitutionMatrixOfC took 0.001 sec + [junit] Testcase: testSimpleProfileProfileAligner took 0.001 sec + [junit] Testcase: testGetTarget took 0.001 sec + [junit] Testcase: testGetMaxScore took 0.001 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: 0.255 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec [junit] - [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.012 sec - [junit] Testcase: testSetDescription took 0.076 sec - [junit] Testcase: testToString took 0.07 sec - [junit] Testcase: testCaseEquivalence took 0.002 sec - [junit] Testcase: test took 0.013 sec - [junit] Testcase: testSimpleSubstitutionMatrix took 0.011 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.005 sec - [junit] Testcase: testSetName took 0.006 sec - [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.011 sec + [junit] Testcase: testSimpleSubstitutionMatrixNotFound took 0.004 sec + [junit] Testcase: testSetDescription took 0.009 sec + [junit] Testcase: testToString took 0.015 sec + [junit] Testcase: testCaseEquivalence took 0.001 sec + [junit] Testcase: test took 0.005 sec + [junit] Testcase: testSimpleSubstitutionMatrix took 0.004 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCStringString took 0.001 sec + [junit] Testcase: testSetName took 0.002 sec + [junit] Testcase: testSimpleSubstitutionMatrixCompoundSetOfCShortShort took 0.001 sec [junit] 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: 0.51 sec - [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.51 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec + [junit] Tests run: 15, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec [junit] - [junit] Testcase: testGetSubstitutionMatrix took 0.185 sec + [junit] Testcase: testGetSubstitutionMatrix took 0.029 sec [junit] Testcase: testGetGapPenalty took 0 sec - [junit] Testcase: testGetComputationTime took 0.054 sec - [junit] Testcase: testGetQuery took 0.005 sec - [junit] Testcase: testGetScore took 0.003 sec - [junit] Testcase: testGetScoreMatrix took 0.003 sec - [junit] Testcase: testGetPair took 0.014 sec - [junit] Testcase: testSmithWaterman took 0.002 sec - [junit] Testcase: testGetProfile took 0.003 sec - [junit] Testcase: testGetMinScore took 0.006 sec - [junit] Testcase: testIsStoringScoreMatrix took 0.001 sec - [junit] Testcase: testGetScoreMatrixAsString took 0.124 sec + [junit] Testcase: testGetComputationTime took 0.01 sec + [junit] Testcase: testGetQuery took 0 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetScoreMatrix took 0.001 sec + [junit] Testcase: testGetPair took 0.002 sec + [junit] Testcase: testSmithWaterman took 0.001 sec + [junit] Testcase: testGetProfile took 0 sec + [junit] Testcase: testGetMinScore took 0 sec + [junit] Testcase: testIsStoringScoreMatrix took 0 sec + [junit] Testcase: testGetScoreMatrixAsString took 0.013 sec [junit] Testcase: testSetStoringScoreMatrix took 0 sec [junit] Testcase: testGetTarget took 0 sec - [junit] Testcase: testGetMaxScore took 0.001 sec + [junit] Testcase: testGetMaxScore took 0 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: 0.417 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.417 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] - [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.005 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 0.002 sec + [junit] Testcase: getSubproblems_should_not_allow_repeated_anchors took 0.002 sec + [junit] Testcase: getCuts_should_return_spaced_cuts_when_query_interval_larger_than_cut_size 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 0.003 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: 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 0.001 sec + [junit] Testcase: getSubproblems_should_not_allow_unalignable_anchors took 0 sec [junit] Running org.biojava.nbio.alignment.routines.GuanUberbacherTest [junit] Testsuite: org.biojava.nbio.alignment.routines.GuanUberbacherTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.269 sec - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.269 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.376 sec [junit] - [junit] Testcase: testGetComputationTime took 0.133 sec - [junit] Testcase: testGuanUberbacher took 0.002 sec - [junit] Testcase: testGetScore took 0.01 sec - [junit] Testcase: testGetPair took 0.012 sec - [junit] Testcase: testGetProfile took 0.003 sec + [junit] Testcase: testGetComputationTime took 0.038 sec + [junit] Testcase: testGuanUberbacher took 0.001 sec + [junit] Testcase: testGetScore took 0.001 sec + [junit] Testcase: testGetPair took 0.005 sec + [junit] Testcase: testGetProfile took 0 sec [junit] Testcase: testGetMinScore took 0.001 sec - [junit] Testcase: should_align_shorter_target took 0.049 sec - [junit] Testcase: should_align_multiple_cuts took 0.002 sec - [junit] Testcase: testGetMaxScore took 0.001 sec - [junit] Testcase: should_align_shorter_query took 0.002 sec + [junit] Testcase: should_align_shorter_target took 0.011 sec + [junit] Testcase: should_align_multiple_cuts took 0 sec + [junit] Testcase: testGetMaxScore took 0 sec + [junit] Testcase: should_align_shorter_query took 0.001 sec BUILD SUCCESSFUL -Total time: 29 seconds +Total time: 6 seconds # Investigate test failure cd biojava-aa-prop && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-aa-prop/build.xml @@ -2618,8 +2653,8 @@ [echo] Using java version 11.0.23 [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: 2.504 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.504 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.313 sec [junit] ------------- Standard Output --------------- [junit] SequenceName,MolecularWeight,ExtinctionCoefficient_True,ExtinctionCoefficient_False,IsoelectricPoint [junit] SAOV_0114,53660.5723,41370.0,41370.0,4.986 @@ -2627,41 +2662,41 @@ [junit] SAA6008_00126,95002.026,55240.0,55740.0,5.7263 [junit] ------------- ---------------- --------------- [junit] - [junit] Testcase: testAdvancedXMLExample took 2.18 sec - [junit] Testcase: testExample1 took 0.101 sec - [junit] Testcase: testExample2 took 0.027 sec - [junit] Testcase: testExample3 took 0.038 sec - [junit] Testcase: testExample1WithCSV took 0.082 sec - [junit] Testcase: testWithCases took 0.021 sec + [junit] Testcase: testAdvancedXMLExample took 0.266 sec + [junit] Testcase: testExample1 took 0.015 sec + [junit] Testcase: testExample2 took 0.004 sec + [junit] Testcase: testExample3 took 0.004 sec + [junit] Testcase: testExample1WithCSV took 0.012 sec + [junit] Testcase: testWithCases took 0.003 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: 3.208 sec - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.208 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.289 sec [junit] - [junit] Testcase: shortExample1 took 0.225 sec - [junit] Testcase: shortExample2 took 2.672 sec - [junit] Testcase: shortExample3 took 0.192 sec - [junit] Testcase: shortExample4 took 0.015 sec - [junit] Testcase: shortExample5 took 0.013 sec + [junit] Testcase: shortExample1 took 0.023 sec + [junit] Testcase: shortExample2 took 0.237 sec + [junit] Testcase: shortExample3 took 0.02 sec + [junit] Testcase: shortExample4 took 0.001 sec + [junit] Testcase: shortExample5 took 0.002 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: 3.671 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.671 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.315 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 3.313 sec - [junit] Testcase: testExample1 took 0.068 sec - [junit] Testcase: testExample2 took 0.051 sec - [junit] Testcase: testExample3 took 0.06 sec - [junit] Testcase: testExample1WithCSV took 0.047 sec - [junit] Testcase: testWithCases took 0.022 sec + [junit] Testcase: testAdvancedXMLExample took 0.276 sec + [junit] Testcase: testExample1 took 0.011 sec + [junit] Testcase: testExample2 took 0.006 sec + [junit] Testcase: testExample3 took 0.004 sec + [junit] Testcase: testExample1WithCSV took 0.006 sec + [junit] Testcase: testWithCases took 0.003 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: 2.486 sec - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.486 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.962 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.962 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. @@ -2876,74 +2911,74 @@ [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 0.237 sec - [junit] Testcase: testMolecularWeightXMLSingleFile took 1.377 sec - [junit] Testcase: testEnrichment took 0.031 sec + [junit] Testcase: testAbsorbance took 0.024 sec + [junit] Testcase: testMolecularWeightXMLSingleFile took 0.234 sec + [junit] Testcase: testEnrichment took 0.005 sec [junit] Testcase: testApliphaticIndex took 0.001 sec - [junit] Testcase: testMolecularWeightXMLNull took 0.037 sec + [junit] Testcase: testMolecularWeightXMLNull took 0.004 sec [junit] Testcase: testApliphaticIndexNull took 0.001 sec - [junit] Testcase: testIsoelectricPointExpasy took 0.011 sec + [junit] Testcase: testIsoelectricPointExpasy took 0.001 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 0.006 sec + [junit] Testcase: testIsoelectricPointNull took 0 sec + [junit] Testcase: testAverageHydropathy took 0 sec + [junit] Testcase: testExtinctionCoefficient took 0 sec [junit] Testcase: testAAComposition took 0.001 sec - [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.093 sec - [junit] Testcase: testMolecularWeight took 0.015 sec - [junit] Testcase: testIsoelectricPointInnovagen took 0.003 sec - [junit] Testcase: testNetChargeNull took 0.011 sec - [junit] Testcase: testExtinctionCoefficientNull took 0.001 sec - [junit] Testcase: testNetCharge took 0.32 sec - [junit] Testcase: testEnrichmentNull took 0.001 sec + [junit] Testcase: testMolecularWeightBasedOnAminoAcidCompositionTable took 0.016 sec + [junit] Testcase: testMolecularWeight took 0 sec + [junit] Testcase: testIsoelectricPointInnovagen took 0.001 sec + [junit] Testcase: testNetChargeNull took 0 sec + [junit] Testcase: testExtinctionCoefficientNull took 0 sec + [junit] Testcase: testNetCharge took 0.039 sec + [junit] Testcase: testEnrichmentNull took 0 sec [junit] Testcase: testInstabilityIndexNull took 0 sec [junit] Testcase: testAverageHydropathyNull took 0.001 sec - [junit] Testcase: testMolecularWeightXML took 0.159 sec - [junit] Testcase: testInstabilityIndex took 0.008 sec + [junit] Testcase: testMolecularWeightXML took 0.025 sec + [junit] Testcase: testInstabilityIndex took 0 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: 0.043 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.111 sec [junit] - [junit] Testcase: testFake took 0.02 sec + [junit] Testcase: testFake took 0.002 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: 0.201 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.201 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] - [junit] Testcase: testFakeTest took 0.081 sec + [junit] Testcase: testFakeTest took 0.011 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: 2.433 sec - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.433 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.353 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 1.041 sec - [junit] Testcase: readWithIDXml took 0.709 sec - [junit] Testcase: readMinXml took 0.244 sec - [junit] Testcase: readAdvancedXml took 0.127 sec - [junit] Testcase: generateXml took 0.104 sec - [junit] Testcase: readXml took 0.153 sec + [junit] Testcase: generateSchema took 0.184 sec + [junit] Testcase: readWithIDXml took 0.075 sec + [junit] Testcase: readMinXml took 0.028 sec + [junit] Testcase: readAdvancedXml took 0.013 sec + [junit] Testcase: generateXml took 0.015 sec + [junit] Testcase: readXml took 0.028 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: 2.395 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.395 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.33 sec [junit] - [junit] Testcase: generateSchema took 1.403 sec - [junit] Testcase: generateXml took 0.244 sec - [junit] Testcase: readXml took 0.687 sec + [junit] Testcase: generateSchema took 0.206 sec + [junit] Testcase: generateXml took 0.035 sec + [junit] Testcase: readXml took 0.083 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: 0.268 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.268 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.05 sec [junit] - [junit] Testcase: testFake took 0.162 sec + [junit] Testcase: testFake took 0.011 sec BUILD SUCCESSFUL -Total time: 50 seconds +Total time: 9 seconds # Skip, missing dependency junitx #cd biojava-genome && ant test cd biojava-phylo && ant test @@ -2960,7 +2995,7 @@ [echo] Using java version 11.0.23 BUILD SUCCESSFUL -Total time: 10 seconds +Total time: 1 second # Native errors may cause issue on NFS...; skipping cd biojava-sequencing && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-sequencing/build.xml @@ -2976,26 +3011,26 @@ [echo] Using java version 11.0.23 [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: 0.587 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.587 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec [junit] - [junit] Testcase: testConvert took 0.458 sec + [junit] Testcase: testConvert took 0.065 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: 0.222 sec - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.222 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] - [junit] Testcase: testBuildAppendSequence took 0.036 sec + [junit] Testcase: testBuildAppendSequence took 0.003 sec [junit] Testcase: testBuildNullDescription took 0 sec [junit] Testcase: testBuildAppendQuality took 0 sec - [junit] Testcase: testBuild took 0.001 sec + [junit] Testcase: testBuild took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsQualityNull took 0 sec - [junit] Testcase: testBuildDefaultVariant took 0.001 sec + [junit] Testcase: testBuildDefaultVariant took 0 sec [junit] Testcase: testBuildMissingQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsBothNull took 0 sec [junit] Testcase: testBuildNullAppendQuality took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths0 took 0 sec - [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0.001 sec + [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengths1 took 0 sec [junit] Testcase: testBuildNullAppendSequence took 0 sec [junit] Testcase: testBuildNonMatchingSequenceQualityScoreLengthsSequenceNull took 0 sec [junit] Testcase: testBuildNullSequence took 0 sec @@ -3008,38 +3043,38 @@ [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: 0.206 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] - [junit] Testcase: testImmutable took 0.02 sec - [junit] Testcase: testBuilder took 0.004 sec + [junit] Testcase: testImmutable took 0.001 sec + [junit] Testcase: testBuilder took 0.001 sec [junit] Testcase: testVariant took 0 sec - [junit] Testcase: testQuality took 0.005 sec - [junit] Testcase: testHashCode took 0.001 sec + [junit] Testcase: testQuality took 0.001 sec + [junit] Testcase: testHashCode took 0 sec [junit] Testcase: testEquals took 0 sec [junit] Testcase: testDescription took 0 sec - [junit] Testcase: testConstructor took 0.001 sec - [junit] Testcase: testSequence took 0 sec + [junit] Testcase: testConstructor took 0 sec + [junit] Testcase: testSequence took 0.001 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: 0.496 sec - [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.496 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec + [junit] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec [junit] - [junit] Testcase: testErrorProbabilitiesNullFastq took 0.01 sec + [junit] Testcase: testErrorProbabilitiesNullFastq took 0.001 sec [junit] Testcase: testErrorProbabilitiesDoubleArray took 0.001 sec [junit] Testcase: testConvertNullVariant took 0 sec [junit] Testcase: testCreateErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.185 sec - [junit] Testcase: testQualityScoresIntArrayNullFastq took 0.001 sec - [junit] Testcase: testQualityScoresQualityScoresTooLarge took 0.001 sec - [junit] Testcase: testQualityScoresQualityScoresTooSmall took 0.001 sec - [junit] Testcase: testQualityScoresNullIntArray took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithErrorProbabilies took 0.03 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: 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 0.001 sec + [junit] Testcase: testConvertQualitiesNullFastq took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSanger took 0 sec [junit] Testcase: testConvertQualitiesIlluminaToSolexa took 0 sec [junit] Testcase: testConvertQualitiesSangerToSolexa took 0 sec @@ -3048,184 +3083,184 @@ [junit] Testcase: testCreateQualityScoresNullFastq took 0 sec [junit] Testcase: testQualityScoresNullFastq took 0 sec [junit] Testcase: testConvertQualitiesSolexaToSanger took 0 sec - [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0.001 sec - [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0 sec - [junit] Testcase: testToListNotAList took 0.002 sec + [junit] Testcase: testCreateDNASequenceWithQualityScoresAndErrorProbabilitiesNullFastq took 0 sec + [junit] Testcase: testErrorProbabilitiesNullErrorProbabilities took 0.001 sec + [junit] Testcase: testToListNotAList took 0.001 sec [junit] Testcase: testConvertQualitiesNullVariant took 0 sec [junit] Testcase: testConvertSameVariant took 0 sec - [junit] Testcase: testQualityScores took 0.006 sec + [junit] Testcase: testQualityScores took 0.003 sec [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooLarge took 0 sec - [junit] Testcase: testErrorProbabilitiesErrorProbabilitiesTooSmall took 0.001 sec - [junit] Testcase: testErrorProbabilitiesDoubleArrayNullFastq 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: testCreateDNASequenceWithQualityScores took 0.001 sec + [junit] Testcase: testCreateDNASequenceWithQualityScores took 0 sec [junit] Testcase: testQualityScoresIntArray took 0 sec [junit] Testcase: testCreateDNASequenceWithErrorProbabilitiesNullFastq took 0 sec - [junit] Testcase: testToList took 0.001 sec + [junit] Testcase: testToList took 0 sec [junit] Testcase: testCreateDNASequenceWithQualityScoresNullFastq took 0 sec - [junit] Testcase: testErrorProbabilities took 0.001 sec + [junit] Testcase: testErrorProbabilities took 0 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.FastqVariantTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.FastqVariantTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.551 sec - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.551 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.366 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.366 sec [junit] - [junit] Testcase: testParseFastqVariant took 0.014 sec - [junit] Testcase: testQualityQualityScoreRoundTrip took 0.002 sec - [junit] Testcase: testQualityLessThanMinimumQualityScore took 0.001 sec - [junit] Testcase: testIsSanger took 0.005 sec - [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0.001 sec + [junit] Testcase: testParseFastqVariant took 0.002 sec + [junit] Testcase: testQualityQualityScoreRoundTrip took 0.001 sec + [junit] Testcase: testQualityLessThanMinimumQualityScore took 0 sec + [junit] Testcase: testIsSanger took 0.002 sec + [junit] Testcase: testQualityMoreThanMaximumQualityScore took 0 sec [junit] Testcase: testIsSolexa took 0 sec - [junit] Testcase: testIsIllumina took 0 sec + [junit] Testcase: testIsIllumina took 0.001 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: 1.918 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.918 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] - [junit] Testcase: testFullRangeAsIllumina took 0.337 sec - [junit] Testcase: testWrappingAsIllumina took 0.014 sec - [junit] Testcase: testValidateDescription took 0.025 sec - [junit] Testcase: testValidateRepeatDescription took 0.005 sec - [junit] Testcase: testMiscDnaAsIllumina took 0.007 sec - [junit] Testcase: testMiscRnaAsIllumina took 0.004 sec - [junit] Testcase: testLongReadsAsIllumina took 0.006 sec - [junit] Testcase: testParseNullReadable took 0.01 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.129 sec - [junit] Testcase: testReadEmptyFile took 0.005 sec - [junit] Testcase: testErrorExamples took 0.097 sec - [junit] Testcase: testParse took 0.002 sec + [junit] Testcase: testFullRangeAsIllumina took 0.021 sec + [junit] Testcase: testWrappingAsIllumina took 0.002 sec + [junit] Testcase: testValidateDescription took 0.005 sec + [junit] Testcase: testValidateRepeatDescription took 0.002 sec + [junit] Testcase: testMiscDnaAsIllumina took 0.001 sec + [junit] Testcase: testMiscRnaAsIllumina took 0.001 sec + [junit] Testcase: testLongReadsAsIllumina took 0.002 sec + [junit] Testcase: testParseNullReadable took 0.001 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.015 sec + [junit] Testcase: testReadEmptyFile took 0 sec + [junit] Testcase: testErrorExamples took 0.01 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: testReadEmptyInputStream took 0.001 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec - [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.006 sec + [junit] Testcase: testWrappedSequence took 0.001 sec + [junit] Testcase: testReadEmptyInputStream took 0 sec + [junit] Testcase: testParseNullParseListener took 0 sec + [junit] Testcase: testReadFile took 0 sec + [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec [junit] Testcase: testReadURL took 0.001 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.002 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec - [junit] Testcase: testWrappedQuality took 0.002 sec + [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec + [junit] Testcase: testWrappedQuality took 0.001 sec [junit] Running org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest [junit] Testsuite: org.biojava.nbio.sequencing.io.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.241 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] - [junit] Testcase: testConvertNotIlluminaVariant took 0.04 sec - [junit] Testcase: testAppendVararg took 0.001 sec + [junit] Testcase: testConvertNotIlluminaVariant took 0.004 sec + [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.017 sec - [junit] Testcase: testWriteFileIterable took 0.07 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec + [junit] Testcase: testWriteFileIterable took 0.014 sec [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.002 sec + [junit] Testcase: testWriteFileVararg took 0.001 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: 1.338 sec - [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.338 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 30, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] - [junit] Testcase: testMiscRnaAsSanger took 0.215 sec - [junit] Testcase: testFullRangeAsSanger took 0.012 sec - [junit] Testcase: testWrappingOriginal took 0.008 sec - [junit] Testcase: testLongReadsOriginal took 0.018 sec - [junit] Testcase: testMiscDnaOriginal took 0.023 sec - [junit] Testcase: testMiscRnaOriginal took 0.019 sec - [junit] Testcase: testValidateDescription took 0.026 sec - [junit] Testcase: testValidateRepeatDescription took 0.001 sec - [junit] Testcase: testFullRangeOriginal took 0.026 sec - [junit] Testcase: testWrappingAsSanger took 0.002 sec - [junit] Testcase: testLongReadsAsSanger took 0.023 sec - [junit] Testcase: testMiscDnaAsSanger took 0.004 sec + [junit] Testcase: testMiscRnaAsSanger took 0.021 sec + [junit] Testcase: testFullRangeAsSanger took 0.002 sec + [junit] Testcase: testWrappingOriginal took 0.002 sec + [junit] Testcase: testLongReadsOriginal took 0.003 sec + [junit] Testcase: testMiscDnaOriginal took 0.001 sec + [junit] Testcase: testMiscRnaOriginal took 0.001 sec + [junit] Testcase: testValidateDescription took 0.004 sec + [junit] Testcase: testValidateRepeatDescription took 0 sec + [junit] Testcase: testFullRangeOriginal took 0.001 sec + [junit] Testcase: testWrappingAsSanger took 0.001 sec + [junit] Testcase: testLongReadsAsSanger took 0.002 sec + [junit] Testcase: testMiscDnaAsSanger took 0.001 sec [junit] Testcase: testParseNullReadable took 0.001 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.296 sec - [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.109 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.014 sec + [junit] Testcase: testReadEmptyFile took 0 sec + [junit] Testcase: testErrorExamples took 0.01 sec [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.001 sec - [junit] Testcase: testReadEmptyInputStream took 0 sec - [junit] Testcase: testParseNullParseListener took 0.001 sec + [junit] Testcase: testWrappedSequence took 0 sec + [junit] Testcase: testReadEmptyInputStream took 0.001 sec + [junit] Testcase: testParseNullParseListener took 0 sec [junit] Testcase: testReadFile took 0 sec - [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testMultipleWrappedQuality took 0.001 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec + [junit] Testcase: testReadEmptyURL took 0 sec [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0.001 sec + [junit] Testcase: testWrappedQuality took 0 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: 0.284 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.116 sec [junit] - [junit] Testcase: testConvertNotSangerVariant took 0.033 sec + [junit] Testcase: testConvertNotSangerVariant took 0.004 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.014 sec - [junit] Testcase: testWriteFileIterable took 0.117 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec + [junit] Testcase: testWriteFileIterable took 0.015 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] 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: 1.14 sec - [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.14 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec + [junit] Tests run: 25, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] - [junit] Testcase: testMiscRnaAsSolexa took 0.348 sec - [junit] Testcase: testFullRangeAsSolexa took 0.036 sec - [junit] Testcase: testValidateDescription took 0.08 sec - [junit] Testcase: testValidateRepeatDescription took 0.027 sec - [junit] Testcase: testWrappingAsSolexa took 0.016 sec - [junit] Testcase: testLongReadsAsSolexa took 0.018 sec - [junit] Testcase: testMiscDnaAsSolexa took 0.002 sec - [junit] Testcase: testParseNullReadable took 0.013 sec - [junit] Testcase: testReadRoundTripSingleFile took 0.171 sec - [junit] Testcase: testReadEmptyFile took 0.001 sec - [junit] Testcase: testErrorExamples took 0.106 sec - [junit] Testcase: testParse took 0.022 sec + [junit] Testcase: testMiscRnaAsSolexa took 0.022 sec + [junit] Testcase: testFullRangeAsSolexa took 0.002 sec + [junit] Testcase: testValidateDescription took 0.005 sec + [junit] Testcase: testValidateRepeatDescription took 0.002 sec + [junit] Testcase: testWrappingAsSolexa took 0.001 sec + [junit] Testcase: testLongReadsAsSolexa took 0.002 sec + [junit] Testcase: testMiscDnaAsSolexa took 0 sec + [junit] Testcase: testParseNullReadable took 0 sec + [junit] Testcase: testReadRoundTripSingleFile took 0.015 sec + [junit] Testcase: testReadEmptyFile took 0 sec + [junit] Testcase: testErrorExamples took 0.011 sec + [junit] Testcase: testParse took 0.001 sec [junit] Testcase: testCreateFastq took 0 sec [junit] Testcase: testReadInputStream took 0 sec - [junit] Testcase: testWrappedSequence took 0.001 sec + [junit] Testcase: testWrappedSequence took 0 sec [junit] Testcase: testReadEmptyInputStream took 0.001 sec [junit] Testcase: testParseNullParseListener took 0 sec - [junit] Testcase: testReadFile took 0.001 sec - [junit] Testcase: testMultipleWrappedQuality took 0.002 sec + [junit] Testcase: testReadFile took 0 sec + [junit] Testcase: testMultipleWrappedQuality took 0 sec [junit] Testcase: testCreateFastqReader took 0 sec - [junit] Testcase: testReadURL took 0.001 sec + [junit] Testcase: testReadURL took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testReadEmptyURL took 0.001 sec - [junit] Testcase: testReadRoundTripMultipleFile took 0.001 sec - [junit] Testcase: testWrappedQuality took 0.003 sec + [junit] Testcase: testReadEmptyURL took 0 sec + [junit] Testcase: testReadRoundTripMultipleFile took 0.002 sec + [junit] Testcase: testWrappedQuality took 0 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: 0.44 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.44 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 sec [junit] - [junit] Testcase: testConvertNotSolexaVariant took 0.042 sec + [junit] Testcase: testConvertNotSolexaVariant took 0.004 sec [junit] Testcase: testAppendVararg took 0 sec [junit] Testcase: testCreateFastq took 0.001 sec - [junit] Testcase: testWriteOutputStreamVararg took 0.006 sec - [junit] Testcase: testWriteFileIterable took 0.181 sec - [junit] Testcase: testWriteOutputStreamIterable took 0.001 sec - [junit] Testcase: testAppendIterable took 0.013 sec + [junit] Testcase: testWriteOutputStreamVararg took 0.002 sec + [junit] Testcase: testWriteFileIterable took 0.013 sec + [junit] Testcase: testWriteOutputStreamIterable took 0 sec + [junit] Testcase: testAppendIterable took 0 sec [junit] Testcase: testCreateFastqWriter took 0 sec - [junit] Testcase: testWriteFileVararg took 0.007 sec + [junit] Testcase: testWriteFileVararg took 0.002 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: 0.119 sec - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] [junit] Testcase: testStreamNullVariant took 0.002 sec - [junit] Testcase: testStreamNullListener took 0.002 sec + [junit] Testcase: testStreamNullListener took 0.001 sec [junit] Testcase: testStreamNullReadable took 0.001 sec BUILD SUCCESSFUL -Total time: 47 seconds +Total time: 6 seconds # Serialization failure in pbuilder mode #cd biojava-modfinder && ant test # Investigate test failure @@ -3246,39 +3281,39 @@ [echo] Using java version 11.0.23 [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: 0.071 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: 0.008 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] - [junit] Testcase: testMe took 0.002 sec + [junit] Testcase: testMe took 0 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: 0.227 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.227 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] - [junit] Testcase: testSomeMethod took 0.022 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: 0.308 sec - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.308 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] - [junit] Testcase: testGetColor took 0.031 sec + [junit] Testcase: testGetColor took 0.002 sec [junit] Testcase: testSetStructure took 0 sec - [junit] Testcase: testClear took 0.001 sec - [junit] Testcase: testGetSelection took 0.029 sec - [junit] Testcase: testRepaint took 0.001 sec + [junit] Testcase: testClear took 0 sec + [junit] Testcase: testGetSelection took 0.001 sec + [junit] Testcase: testRepaint took 0 sec [junit] Testcase: testSetSelection took 0 sec [junit] Testcase: testSetZoom took 0 sec [junit] Testcase: testSetColor took 0 sec - [junit] Testcase: testSetStyle took 0.001 sec + [junit] Testcase: testSetStyle took 0 sec [junit] Running org.biojava.nbio.structure.gui.ViewerTest [junit] Testsuite: org.biojava.nbio.structure.gui.ViewerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.1 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.136 sec [junit] [junit] Testcase: testStructureLoad took 0.001 sec BUILD SUCCESSFUL -Total time: 25 seconds +Total time: 2 seconds cd biojava-ontology && ant test Buildfile: /build/reproducible-path/biojava4-live-4.2.12+dfsg/biojava-ontology/build.xml @@ -3293,7 +3328,7 @@ [echo] Using java version 11.0.23 BUILD SUCCESSFUL -Total time: 16 seconds +Total time: 1 second make[1]: Leaving directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -3304,7 +3339,7 @@ dh_install debian/rules override_jh_installjavadoc make[1]: Entering directory '/build/reproducible-path/biojava4-live-4.2.12+dfsg' -dpkg: warning: --compare-versions used with obsolete relation operator '>' +dpkg: hoiatus: --compare-versions used with obsolete relation operator '>' 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) \ @@ -3351,12 +3386,14 @@ 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/522086/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/522086/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/400204 and its subdirectories -I: Current time: Wed Aug 7 07:39:41 -12 2024 -I: pbuilder-time-stamp: 1723059581 +I: removing directory /srv/workspace/pbuilder/522086 and its subdirectories +I: Current time: Wed Sep 10 16:06:36 +14 2025 +I: pbuilder-time-stamp: 1757469996