Diff of the two buildlogs: -- --- b1/build.log 2020-05-24 21:48:58.853664469 +0000 +++ b2/build.log 2020-05-24 22:19:38.761026555 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 24 09:29:05 -12 2020 -I: pbuilder-time-stamp: 1590355745 +I: Current time: Mon May 25 11:49:24 +14 2020 +I: pbuilder-time-stamp: 1590356964 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Mon Nov 12 03:36:34 2018 -12 +gpgv: Signature made Tue Nov 13 05:36:34 2018 +14 gpgv: using RSA key 5FB46F83D3B952046335D26D78DC68DB326D8438 gpgv: issuer "osallou@debian.org" gpgv: Can't check signature: No public key @@ -31,6 +31,170 @@ dpkg-source: info: applying java8_instead_of_11.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/27025/tmp/hooks/D01_modify_environment starting +debug: Running on ff2a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27025/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27025/tmp/hooks/D02_print_environment starting +I: set + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf + IFS=' + ' + INVOCATION_ID=4c7728bdac8041cebcd37e96f7bfc318 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27025 + PS4='+ ' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.WskL1a31YZ/pbuilderrc_SRhK --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WskL1a31YZ/b2 --logfile b2/build.log biojava-live_1.7.1-8.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ +I: uname -a + Linux i-capture-the-hostname 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux +I: ls -l /bin + total 3328 + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 May 25 11:50 sh -> bash + lrwxrwxrwx 1 root root 4 May 23 22:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/27025/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -206,7 +370,7 @@ Get: 120 http://deb.debian.org/debian buster/main armhf libwebsocket-api-java all 1.1-1+deb10u1 [40.0 kB] Get: 121 http://deb.debian.org/debian buster/main armhf libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 122 http://deb.debian.org/debian buster/main armhf libhsqldb-java all 2.4.1-2 [1633 kB] -Fetched 269 MB in 34s (7885 kB/s) +Fetched 269 MB in 29s (9257 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) @@ -737,134 +901,134 @@ update-alternatives: using /usr/lib/jvm/java-11-openjdk-armhf/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:SecureSign_RootCA11.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:USERTrust_ECC_Certification_Authority.pem +Adding debian:XRamp_Global_CA_Root.pem +Adding debian:AC_RAIZ_FNMT-RCM.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:LuxTrust_Global_Root_2.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:AffirmTrust_Premium.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:EE_Certification_Centre_Root_CA.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:GeoTrust_Universal_CA_2.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:GeoTrust_Primary_Certification_Authority.pem +Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:Secure_Global_CA.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Certplus_Class_2_Primary_CA.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:COMODO_ECC_Certification_Authority.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem -Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Amazon_Root_CA_2.pem Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:Starfield_Class_2_CA.pem -Adding debian:Certigna.pem -Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:thawte_Primary_Root_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:AddTrust_External_Root.pem -Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem -Adding debian:GeoTrust_Global_CA.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Certinomis_-_Root_CA.pem -Adding debian:LuxTrust_Global_Root_2.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:EE_Certification_Centre_Root_CA.pem +Adding debian:T-TeleSec_GlobalRoot_Class_2.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem -Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem -Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:Entrust_Root_Certification_Authority_-_G2.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:Taiwan_GRCA.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:thawte_Primary_Root_CA.pem +Adding debian:DST_Root_CA_X3.pem +Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem +Adding debian:SecureTrust_CA.pem Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:EC-ACC.pem -Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem -Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:Buypass_Class_2_Root_CA.pem -Adding debian:GeoTrust_Primary_Certification_Authority.pem -Adding debian:thawte_Primary_Root_CA_-_G2.pem -Adding debian:XRamp_Global_CA_Root.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:Security_Communication_RootCA2.pem +Adding debian:Amazon_Root_CA_1.pem +Adding debian:GeoTrust_Universal_CA.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:thawte_Primary_Root_CA_-_G3.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Baltimore_CyberTrust_Root.pem -Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:ePKI_Root_Certification_Authority.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:COMODO_RSA_Certification_Authority.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem -Adding debian:Deutsche_Telekom_Root_CA_2.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem -Adding debian:Izenpe.com.pem Adding debian:AffirmTrust_Commercial.pem -Adding debian:certSIGN_ROOT_CA.pem +Adding debian:TWCA_Global_Root_CA.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:thawte_Primary_Root_CA_-_G2.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:E-Tugra_Certification_Authority.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:GlobalSign_Root_CA.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem +Adding debian:Izenpe.com.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:EC-ACC.pem +Adding debian:DigiCert_Assured_ID_Root_G2.pem +Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:Certinomis_-_Root_CA.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:AddTrust_External_Root.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:CA_Disig_Root_R2.pem +Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:ISRG_Root_X1.pem -Adding debian:GeoTrust_Universal_CA.pem -Adding debian:TrustCor_ECA-1.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:QuoVadis_Root_CA_3.pem +Adding debian:GeoTrust_Global_CA.pem +Adding debian:Secure_Global_CA.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:Deutsche_Telekom_Root_CA_2.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:Certum_Trusted_Network_CA_2.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem +Adding debian:Certigna.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:Taiwan_GRCA.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:SecureTrust_CA.pem +Adding debian:certSIGN_ROOT_CA.pem Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:GeoTrust_Universal_CA_2.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem +Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem done. Setting up libbytecode-java (0.92.svn.20090106-2) ... Setting up junit4 (4.12-8) ... @@ -893,7 +1057,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/biojava-live-1.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/biojava-live-1.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package biojava-live dpkg-buildpackage: info: source version 1:1.7.1-8 dpkg-buildpackage: info: source distribution unstable @@ -917,7 +1081,7 @@ clean: BUILD SUCCESSFUL -Total time: 4 seconds +Total time: 10 seconds debian/rules override_dh_clean make[1]: Entering directory '/build/biojava-live-1.7.1' ant clean # most probably this is not needed when using dh - leave it to be sure ... @@ -934,7 +1098,7 @@ clean: BUILD SUCCESSFUL -Total time: 4 seconds +Total time: 10 seconds dh_clean make[1]: Leaving directory '/build/biojava-live-1.7.1' debian/rules build @@ -994,7 +1158,7 @@ [jar] Building jar: /build/biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL -Total time: 3 minutes 28 seconds +Total time: 5 minutes 20 seconds # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1017,7 +1181,7 @@ package-biojava: BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 25 seconds #ant compile-demos ant javadocs-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1260,10 +1424,10 @@ [javadoc] javadoc: warning - invalid usage of tag &cvsroot [javadoc] javadoc: warning - invalid usage of tag &content [javadoc] Generating /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/package-summary.html... - [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/bibobjects_java.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... + [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_corba.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... + [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/bibobjects_java.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_soap.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... - [javadoc] Copying file /build/biojava-live-1.7.1/src/org/biojava/bibliography/doc-files/BibRefQuery_simple.jpg to directory /build/biojava-live-1.7.1/ant-build/docs/biojava/org/biojava/bibliography/doc-files... [javadoc] Building index for all the packages and classes... [javadoc] Building index for all classes... [javadoc] Building index for all classes... @@ -1272,7 +1436,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 4 minutes 24 seconds +Total time: 7 minutes 1 second touch build-stamp make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_auto_test @@ -1333,357 +1497,357 @@ runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.203 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.136 sec [junit] Running org.biojava.bio.MergeAnnotationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.23 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] Running org.biojava.bio.dist.DistSerTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.781 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.41 sec [junit] Running org.biojava.bio.dist.DistributionTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.895 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.362 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] Running org.biojava.bio.dp.DPSerializationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.841 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.55 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.885 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec [junit] Running org.biojava.bio.program.fastq.FastqTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.295 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.791 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.125 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest - [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec + [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.321 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.208 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.24 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.145 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.129 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojava.bio.program.sax.BlastTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.33 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.51 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.975 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.829 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.816 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.474 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.649 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.024 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.136 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.642 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.319 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.819 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.238 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.973 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.049 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.306 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.586 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.763 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.953 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.599 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.216 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.287 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 10.469 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.644 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.681 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.545 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.555 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.821 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.273 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.525 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.34 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.732 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 8.724 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 25.736 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.647 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.915 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.164 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.919 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.203 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest - [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.176 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.141 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.06 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.255 sec [junit] Running org.biojava.bio.seq.DNAToolsTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.175 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.11 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.202 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.293 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.785 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.RNAToolsTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.048 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.527 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.45 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.138 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.16 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest - [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 2.922 sec + [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 2.985 sec [junit] Test org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest FAILED [junit] Running org.biojava.bio.seq.db.emblcd.DivisionLkpReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.148 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.804 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.166 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.07 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.397 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.319 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.063 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.058 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest - [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.738 sec + [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.344 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest - [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 7.43 sec + [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 6.307 sec [junit] Test org.biojava.bio.seq.io.SeqIOToolsTest FAILED [junit] Running org.biojava.bio.seq.io.SmartSequenceBuilderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.851 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.468 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.332 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.858 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec [junit] Running org.biojava.bio.structure.MMcifTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 39.546 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.034 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.433 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.527 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.466 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.77 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest - [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 29.578 sec + [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 30.003 sec [junit] Test org.biojava.bio.structure.StructurePairAlignerTest FAILED [junit] Running org.biojava.bio.structure.StructureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.348 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.52 sec [junit] Running org.biojava.bio.structure.StructureToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.077 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.316 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.276 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.438 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.569 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.029 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.127 sec [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.914 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.283 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.157 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.907 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.02 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 17.379 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.244 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] Running org.biojava.bio.symbol.GappedSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.symbol.PointLocationTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.097 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.SymbolListTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.716 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.833 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Running org.biojava.bio.symbol.TranslationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.999 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.63 sec [junit] Running org.biojava.directory.OBDARegistryParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.18 sec [junit] Running org.biojava.directory.RegistryConfigurationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec [junit] Running org.biojava.directory.SystemRegistryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.563 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.023 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.475 sec [junit] Running org.biojava.naming.ObdaUriParserTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.ontology.OntologyTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.037 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] Running org.biojava.ontology.ParseOBOFileTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.811 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.32 sec [junit] Running org.biojava.ontology.TermImplTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.ontology.TripleImplTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.utils.ListToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec [junit] Running org.biojava.utils.SmallMapTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.utils.automata.NfaTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.utils.process.ExternalProcessTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.279 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.793 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.09 sec [junit] Running org.biojava.utils.regex.RegexTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.137 sec [junit] Running org.biojava.utils.walker.WalkerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.096 sec [junit] Running org.biojavax.EmptyRichAnnotationTest - [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.023 sec + [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] Running org.biojavax.SimpleCommentTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec [junit] Running org.biojavax.SimpleCrossRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.597 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.033 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.262 sec [junit] Running org.biojavax.SimpleDocRefTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.046 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.172 sec [junit] Running org.biojavax.SimpleNamespaceTest - [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.057 sec + [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.128 sec [junit] Test org.biojavax.SimpleNamespaceTest FAILED [junit] Running org.biojavax.SimpleNoteTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec [junit] Running org.biojavax.SimpleRankedDocRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.072 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.216 sec [junit] Running org.biojavax.SimpleRichAnnotationTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec [junit] Running org.biojavax.bio.SimpleBioEntryTest - [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.087 sec + [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.166 sec [junit] Test org.biojavax.bio.SimpleBioEntryTest FAILED [junit] Running org.biojavax.bio.seq.CompoundRichLocationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.106 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.284 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.391 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.965 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.487 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.956 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.099 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.254 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.039 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.405 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.108 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.433 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.446 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.191 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.161 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.54 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.056 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.214 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojavax.ga.util.GAToolsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojavax.ga.util.WeightedSetTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.ontology.SimpleComparableOntologyTest - [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.051 sec + [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.131 sec [junit] Running org.biojavax.ontology.SimpleComparableTermTest - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec BUILD SUCCESSFUL -Total time: 5 minutes 8 seconds +Total time: 5 minutes 43 seconds make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_installdocs dh_installchangelogs @@ -1713,22 +1877,24 @@ dpkg-gencontrol: warning: Depends field of package libbiojava1.7-java: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb +dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-8_all.deb'. dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_1.7.1-8_all.deb'. -dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-8_all.deb'. dpkg-deb: building package 'libbiojava-java-doc' in '../libbiojava-java-doc_1.7.1-8_all.deb'. -dpkg-deb: building package 'libbiojava-java' in '../libbiojava-java_1.7.1-8_all.deb'. +dpkg-deb: building package 'libbiojava1.7-java' in '../libbiojava1.7-java_1.7.1-8_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava-live_1.7.1-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/27025/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27025/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/6775 and its subdirectories -I: Current time: Sun May 24 09:48:54 -12 2020 -I: pbuilder-time-stamp: 1590356934 +I: removing directory /srv/workspace/pbuilder/27025 and its subdirectories +I: Current time: Mon May 25 12:19:32 +14 2020 +I: pbuilder-time-stamp: 1590358772