Diff of the two buildlogs: -- --- b1/build.log 2019-06-24 12:22:35.447888078 +0000 +++ b2/build.log 2019-06-24 13:04:39.171998277 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 26 06:43:24 -12 2020 -I: pbuilder-time-stamp: 1595789004 +I: Current time: Tue Jun 25 02:22:57 +14 2019 +I: pbuilder-time-stamp: 1561378977 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ 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 @@ -32,6 +32,18 @@ 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/26242/tmp/hooks/D01_modify_environment starting +disorder-fs debug: Running on profitbricks-build12-i386. +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/26242/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -281,7 +293,7 @@ Get: 194 http://cdn-fastly.deb.debian.org/debian buster/main i386 libwebsocket-api-java all 1.1-1 [39.8 kB] Get: 195 http://cdn-fastly.deb.debian.org/debian buster/main i386 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 196 http://cdn-fastly.deb.debian.org/debian buster/main i386 libhsqldb-java all 2.4.1-2 [1633 kB] -Fetched 402 MB in 28s (14.4 MB/s) +Fetched 402 MB in 5min 47s (1159 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:i386. (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 ... 19231 files and directories currently installed.) @@ -1125,134 +1137,134 @@ update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/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:COMODO_RSA_Certification_Authority.pem -Adding debian:IdenTrust_Commercial_Root_CA_1.pem -Adding debian:Security_Communication_Root_CA.pem -Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Comodo_AAA_Services_root.pem +Adding debian:QuoVadis_Root_CA_2_G3.pem +Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem +Adding debian:CA_Disig_Root_R2.pem +Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:DigiCert_Assured_ID_Root_CA.pem +Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem +Adding debian:SecureSign_RootCA11.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem +Adding debian:SecureTrust_CA.pem +Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem -Adding debian:Actalis_Authentication_Root_CA.pem -Adding debian:TWCA_Global_Root_CA.pem -Adding debian:thawte_Primary_Root_CA_-_G3.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem +Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem +Adding debian:certSIGN_ROOT_CA.pem +Adding debian:T-TeleSec_GlobalRoot_Class_3.pem +Adding debian:QuoVadis_Root_CA.pem +Adding debian:TrustCor_RootCert_CA-1.pem +Adding debian:DST_Root_CA_X3.pem Adding debian:Certplus_Class_2_Primary_CA.pem -Adding debian:COMODO_Certification_Authority.pem -Adding debian:ISRG_Root_X1.pem -Adding debian:Sonera_Class_2_Root_CA.pem -Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem +Adding debian:AffirmTrust_Commercial.pem +Adding debian:GeoTrust_Universal_CA_2.pem +Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem +Adding debian:USERTrust_RSA_Certification_Authority.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem +Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem +Adding debian:AffirmTrust_Networking.pem +Adding debian:Certum_Trusted_Network_CA.pem +Adding debian:IdenTrust_Commercial_Root_CA_1.pem +Adding debian:TeliaSonera_Root_CA_v1.pem +Adding debian:AffirmTrust_Premium.pem +Adding debian:Certigna.pem +Adding debian:Chambers_of_Commerce_Root_-_2008.pem +Adding debian:GlobalSign_Root_CA_-_R6.pem +Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem +Adding debian:Atos_TrustedRoot_2011.pem +Adding debian:Starfield_Class_2_CA.pem +Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem +Adding debian:GeoTrust_Global_CA.pem +Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Secure_Global_CA.pem -Adding debian:SwissSign_Gold_CA_-_G2.pem +Adding debian:Amazon_Root_CA_3.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem +Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem -Adding debian:QuoVadis_Root_CA_2.pem -Adding debian:Amazon_Root_CA_2.pem -Adding debian:Global_Chambersign_Root_-_2008.pem -Adding debian:EC-ACC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem -Adding debian:T-TeleSec_GlobalRoot_Class_3.pem -Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem -Adding debian:Buypass_Class_3_Root_CA.pem -Adding debian:COMODO_ECC_Certification_Authority.pem +Adding debian:Baltimore_CyberTrust_Root.pem +Adding debian:SZAFIR_ROOT_CA2.pem +Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:USERTrust_ECC_Certification_Authority.pem -Adding debian:Certigna.pem +Adding debian:TrustCor_RootCert_CA-2.pem +Adding debian:DigiCert_Global_Root_CA.pem +Adding debian:QuoVadis_Root_CA_2.pem +Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:thawte_Primary_Root_CA.pem -Adding debian:AffirmTrust_Premium.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem +Adding debian:COMODO_RSA_Certification_Authority.pem +Adding debian:GeoTrust_Primary_Certification_Authority.pem +Adding debian:Cybertrust_Global_Root.pem +Adding debian:Microsec_e-Szigno_Root_CA_2009.pem +Adding debian:Trustis_FPS_Root_CA.pem +Adding debian:DigiCert_Global_Root_G3.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem +Adding debian:Deutsche_Telekom_Root_CA_2.pem +Adding debian:Taiwan_GRCA.pem +Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_3.pem -Adding debian:AddTrust_External_Root.pem +Adding debian:Izenpe.com.pem +Adding debian:GDCA_TrustAUTH_R5_ROOT.pem +Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem +Adding debian:Sonera_Class_2_Root_CA.pem +Adding debian:VeriSign_Universal_Root_Certification_Authority.pem +Adding debian:ACCVRAIZ1.pem +Adding debian:GeoTrust_Universal_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem -Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem -Adding debian:Trustis_FPS_Root_CA.pem -Adding debian:TrustCor_RootCert_CA-1.pem -Adding debian:QuoVadis_Root_CA_2_G3.pem -Adding debian:TrustCor_ECA-1.pem -Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:DigiCert_Global_Root_G2.pem +Adding debian:AffirmTrust_Premium_ECC.pem +Adding debian:Hongkong_Post_Root_CA_1.pem +Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem +Adding debian:Buypass_Class_3_Root_CA.pem +Adding debian:GlobalSign_Root_CA.pem +Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem +Adding debian:CFCA_EV_ROOT.pem +Adding debian:TWCA_Root_Certification_Authority.pem +Adding debian:Global_Chambersign_Root_-_2008.pem +Adding debian:Security_Communication_RootCA2.pem +Adding debian:COMODO_Certification_Authority.pem +Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem +Adding debian:ISRG_Root_X1.pem +Adding debian:QuoVadis_Root_CA_3_G3.pem +Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem -Adding debian:ACCVRAIZ1.pem -Adding debian:SSL.com_Root_Certification_Authority_RSA.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem -Adding debian:DigiCert_Trusted_Root_G4.pem +Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem -Adding debian:SSL.com_Root_Certification_Authority_ECC.pem +Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem +Adding debian:Actalis_Authentication_Root_CA.pem +Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:TrustCor_ECA-1.pem +Adding debian:Amazon_Root_CA_4.pem +Adding debian:EC-ACC.pem +Adding debian:Amazon_Root_CA_2.pem +Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem -Adding debian:Network_Solutions_Certificate_Authority.pem -Adding debian:TWCA_Root_Certification_Authority.pem -Adding debian:GlobalSign_Root_CA.pem -Adding debian:Security_Communication_RootCA2.pem Adding debian:AC_RAIZ_FNMT-RCM.pem -Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem -Adding debian:AffirmTrust_Premium_ECC.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem -Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem -Adding debian:Taiwan_GRCA.pem -Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem -Adding debian:Certum_Trusted_Network_CA.pem -Adding debian:SZAFIR_ROOT_CA2.pem -Adding debian:AffirmTrust_Networking.pem -Adding debian:Go_Daddy_Class_2_CA.pem -Adding debian:Cybertrust_Global_Root.pem -Adding debian:DigiCert_Assured_ID_Root_CA.pem -Adding debian:GeoTrust_Universal_CA_2.pem -Adding debian:Starfield_Class_2_CA.pem +Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem -Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem -Adding debian:SecureTrust_CA.pem -Adding debian:GlobalSign_Root_CA_-_R3.pem +Adding debian:Certinomis_-_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem -Adding debian:GeoTrust_Global_CA.pem -Adding debian:DigiCert_Global_Root_CA.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem -Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem +Adding debian:AddTrust_External_Root.pem +Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem +Adding debian:Network_Solutions_Certificate_Authority.pem +Adding debian:Entrust_Root_Certification_Authority.pem +Adding debian:Amazon_Root_CA_1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem -Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem -Adding debian:Buypass_Class_2_Root_CA.pem +Adding debian:ePKI_Root_Certification_Authority.pem +Adding debian:SSL.com_Root_Certification_Authority_RSA.pem +Adding debian:Go_Daddy_Class_2_CA.pem +Adding debian:thawte_Primary_Root_CA_-_G3.pem +Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Certum_Trusted_Network_CA_2.pem -Adding debian:Entrust_Root_Certification_Authority.pem -Adding debian:Izenpe.com.pem -Adding debian:certSIGN_ROOT_CA.pem -Adding debian:Deutsche_Telekom_Root_CA_2.pem -Adding debian:DigiCert_Assured_ID_Root_G3.pem -Adding debian:TrustCor_RootCert_CA-2.pem -Adding debian:CFCA_EV_ROOT.pem -Adding debian:Amazon_Root_CA_4.pem -Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem -Adding debian:USERTrust_RSA_Certification_Authority.pem -Adding debian:Amazon_Root_CA_1.pem -Adding debian:Atos_TrustedRoot_2011.pem -Adding debian:GDCA_TrustAUTH_R5_ROOT.pem -Adding debian:Hongkong_Post_Root_CA_1.pem -Adding debian:QuoVadis_Root_CA.pem -Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem -Adding debian:AffirmTrust_Commercial.pem -Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem -Adding debian:EE_Certification_Centre_Root_CA.pem -Adding debian:Microsec_e-Szigno_Root_CA_2009.pem -Adding debian:CA_Disig_Root_R2.pem -Adding debian:Amazon_Root_CA_3.pem -Adding debian:GeoTrust_Universal_CA.pem -Adding debian:DigiCert_Global_Root_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem -Adding debian:QuoVadis_Root_CA_3_G3.pem -Adding debian:LuxTrust_Global_Root_2.pem -Adding debian:DST_Root_CA_X3.pem -Adding debian:Certinomis_-_Root_CA.pem -Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem -Adding debian:Chambers_of_Commerce_Root_-_2008.pem -Adding debian:GeoTrust_Primary_Certification_Authority.pem -Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem -Adding debian:SecureSign_RootCA11.pem -Adding debian:GlobalSign_Root_CA_-_R6.pem -Adding debian:VeriSign_Universal_Root_Certification_Authority.pem -Adding debian:DigiCert_Global_Root_G3.pem -Adding debian:QuoVadis_Root_CA_1_G3.pem -Adding debian:Comodo_AAA_Services_root.pem -Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem -Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem -Adding debian:TeliaSonera_Root_CA_v1.pem -Adding debian:SwissSign_Silver_CA_-_G2.pem -Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem -Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem -Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem -Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem +Adding debian:E-Tugra_Certification_Authority.pem +Adding debian:Security_Communication_Root_CA.pem +Adding debian:COMODO_ECC_Certification_Authority.pem done. Setting up libbytecode-java (0.92.svn.20090106-2) ... Setting up junit4 (4.12-8) ... @@ -1280,9 +1292,41 @@ Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). -0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 182 kB of additional disk space will be used. +Get:1 http://cdn-fastly.deb.debian.org/debian buster/main i386 libnumber-compare-perl all 0.03-1 [7642 B] +Get:2 http://cdn-fastly.deb.debian.org/debian buster/main i386 libtext-glob-perl all 0.10-1 [8362 B] +Get:3 http://cdn-fastly.deb.debian.org/debian buster/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://cdn-fastly.deb.debian.org/debian buster/main i386 usrmerge all 21 [12.8 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (79.9 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 32499 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.10-1_all.deb ... +Unpacking libtext-glob-perl (0.10-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_21_all.deb ... +Unpacking usrmerge (21) ... +Setting up libtext-glob-perl (0.10-1) ... +Setting up libnumber-compare-perl (0.03-1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (21) ... +The system has been successfully converted. +Processing triggers for man-db (2.8.5-2) ... +Not building database; man-db/auto-update is not 'true'. 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 @@ -1306,7 +1350,7 @@ clean: BUILD SUCCESSFUL -Total time: 0 seconds +Total time: 1 second 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 ... @@ -1383,7 +1427,7 @@ [jar] Building jar: /build/biojava-live-1.7.1/ant-build/biojava.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 4 minutes 10 seconds # Add here commands to compile the package. ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1406,7 +1450,7 @@ package-biojava: BUILD SUCCESSFUL -Total time: 0 seconds +Total time: 24 seconds #ant compile-demos ant javadocs-biojava Buildfile: /build/biojava-live-1.7.1/build.xml @@ -1649,10 +1693,10 @@ [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/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_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_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/BibRefQuery_soap.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... @@ -1661,7 +1705,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 12 seconds +Total time: 6 minutes 4 seconds touch build-stamp make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_auto_test @@ -1722,357 +1766,357 @@ runtests: [echo] Running tests: ** [junit] Running org.biojava.bio.AnnotationTypeTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.053 sec [junit] Running org.biojava.bio.MergeAnnotationTest - [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: 0.016 sec [junit] Running org.biojava.bio.alignment.FlexibleAlignmentTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.alignment.SubstitutionMatrixTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.bio.dist.DistSerTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.064 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.151 sec [junit] Running org.biojava.bio.dist.DistributionTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.dist.DistributionToolsTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.022 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 sec [junit] Running org.biojava.bio.dist.TranslatedDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.dp.DPSerializationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.109 sec [junit] Running org.biojava.bio.dp.EmissionStateEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.dp.MarkovModelEventTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeManagerTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.031 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.119 sec [junit] Running org.biojava.bio.molbio.RestrictionEnzymeTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.program.fastq.FastqBuilderTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojava.bio.program.fastq.FastqTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.program.fastq.FastqVariantTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] Running org.biojava.bio.program.fastq.IlluminaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqReaderTest - [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 27, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] Running org.biojava.bio.program.fastq.SangerFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.073 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqReaderTest - [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 22, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.146 sec [junit] Running org.biojava.bio.program.fastq.SolexaFastqWriterTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec [junit] Running org.biojava.bio.program.indexdb.IndexToolsTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.08 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.646 sec [junit] Running org.biojava.bio.program.phred.PhredToolsTest - [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: 0.025 sec [junit] Running org.biojava.bio.program.sax.BlastTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.354 sec [junit] Running org.biojava.bio.program.sax.blastxml.BlastXMLTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec [junit] Running org.biojava.bio.program.ssbind.SSBindFasta3_3t08Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.204 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.404 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.171 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.326 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.297 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.507 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastp2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.318 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.497 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.341 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.5 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBIblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.324 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.478 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.32 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.521 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastn2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.329 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.563 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_0_11Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.824 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.432 sec [junit] Running org.biojava.bio.program.ssbind.SSBindNCBItblastx2_2_3Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.167 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.046 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.098 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastp2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.041 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.066 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.083 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastn2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.662 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.243 sec [junit] Running org.biojava.bio.program.ssbind.SSBindWUtblastx2_0a19Test - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.142 sec [junit] Running org.biojava.bio.proteomics.IsoelectricPointCalcTest - [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: 0.011 sec [junit] Running org.biojava.bio.proteomics.MassCalcTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexStreamReaderTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.054 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.089 sec [junit] Running org.biojava.bio.proteomics.aaindex.AAindexTest - [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.proteomics.aaindex.SimpleSymbolPropertyTableDBTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.search.MaxMismatchPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.search.SeqContentPatternTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchHitTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchResultTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.bio.search.SimpleSeqSimilaritySearchSubHitTest [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.seq.CircularSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.032 sec [junit] Running org.biojava.bio.seq.DNAToolsTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.seq.FeatureFilterTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.026 sec [junit] Running org.biojava.bio.seq.FeatureHolderUtilsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.seq.FilterUtilsTest - [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec + [junit] Tests run: 23, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.038 sec [junit] Running org.biojava.bio.seq.MergeFeatureHolderTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.seq.NewSimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.088 sec [junit] Running org.biojava.bio.seq.ProteinToolsTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.seq.RNAToolsTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] Running org.biojava.bio.seq.SeqSerializationTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.079 sec [junit] Running org.biojava.bio.seq.SimpleAssemblyTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.seq.db.EmblCDROMIndexStoreTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec [junit] Running org.biojava.bio.seq.db.HashSequenceDBTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.seq.db.biosql.BioSQLSequenceDBTest - [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 0.272 sec + [junit] Tests run: 5, Failures: 0, Errors: 5, Skipped: 0, Time elapsed: 0.622 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: 0.002 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamIdxReaderTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.seq.db.emblcd.EntryNamRandomAccessTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.bio.seq.filter.FilterTransformerTest - [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: 0.025 sec [junit] Running org.biojava.bio.seq.homol.SimpleSimilarityPairFeatureTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.bio.seq.impl.GappedSequenceTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.bio.seq.impl.SubSequenceTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] Running org.biojava.bio.seq.impl.ViewSeqSerializationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.047 sec [junit] Running org.biojava.bio.seq.impl.ViewSequenceTest - [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: 0.016 sec [junit] Running org.biojava.bio.seq.io.LocationFormatterTest - [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec + [junit] Tests run: 26, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.084 sec [junit] Running org.biojava.bio.seq.io.MSFAlignmentFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.seq.io.SeqIOToolsTest - [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.275 sec + [junit] Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.566 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: 0.424 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.757 sec [junit] Running org.biojava.bio.seq.io.SymbolListCharSequenceTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojava.bio.seq.io.filterxml.FilterXMLTest - [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec + [junit] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.093 sec [junit] Running org.biojava.bio.seq.project.ProjectedFeatureHolderTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.bio.structure.MMcifTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.298 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.69 sec [junit] Running org.biojava.bio.structure.PDBFileParserTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.bio.structure.PdbFileFormat30Test - [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: 0.056 sec [junit] Running org.biojava.bio.structure.SourceCompoundTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.206 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 sec [junit] Running org.biojava.bio.structure.StructurePairAlignerTest - [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.026 sec + [junit] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 1.837 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: 0.024 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 sec [junit] Running org.biojava.bio.structure.StructureToolsTest - [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: 0.02 sec [junit] Running org.biojava.bio.symbol.AlphabetManagerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.AlphabetSerializationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] Running org.biojava.bio.symbol.BetweenLocationTest - [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 34, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.symbol.CircularLocationTest - [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.symbol.CodonPrefToolsTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.04 sec [junit] Running org.biojava.bio.symbol.CompoundLocationTest - [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec + [junit] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.028 sec [junit] Running org.biojava.bio.symbol.CrossProductAlphabetIndexTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.878 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.278 sec [junit] Running org.biojava.bio.symbol.CrossProductTokenizationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.019 sec [junit] Running org.biojava.bio.symbol.DoubleAlphabetTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.FundamentalAtomicSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.GappedSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.IndexedNoAmbPackTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojava.bio.symbol.IntegerAlphabetTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.LinearAlphabetIndexTest [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MergeLocationTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec [junit] Running org.biojava.bio.symbol.MotifToolsTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec [junit] Running org.biojava.bio.symbol.NameTokenizationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojava.bio.symbol.PointLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.RangeLocationTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.SimpleAtomicSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.SimpleBasisSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.SimpleCodonPrefTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolEventTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.SimpleSymbolListTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.bio.symbol.SimpleWobbleDistributionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.bio.symbol.SymbolListTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.305 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.548 sec [junit] Running org.biojava.bio.symbol.SymbolSerializationTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojava.bio.symbol.TranslationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec [junit] Running org.biojava.bio.symbol.UkkonenSuffixTreeTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.044 sec [junit] Running org.biojava.directory.OBDARegistryParserTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.directory.RegistryConfigurationTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojava.directory.SystemRegistryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.naming.ObdaInitialContextFactoryTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.118 sec [junit] Running org.biojava.naming.ObdaUriParserTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.ontology.OntologyTest - [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 21, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.ontology.ParseOBOFileTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.061 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.135 sec [junit] Running org.biojava.ontology.TermImplTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojava.ontology.TripleImplTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.utils.RepeatedCharSequenceTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojava.utils.SmallMapTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec [junit] Running org.biojava.utils.automata.NfaTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec [junit] Running org.biojava.utils.lsid.LifeScienceIdentifierTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec [junit] Running org.biojava.utils.process.ExternalProcessTest - [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec + [junit] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.086 sec [junit] Running org.biojava.utils.regex.PatternCheckerTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.013 sec [junit] Running org.biojava.utils.regex.RegexTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojava.utils.walker.WalkerFactoryTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 sec [junit] Running org.biojava.utils.walker.WalkerTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojavax.CrossReferenceResolutionExceptionTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.DummyCrossReferenceResolverTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.014 sec [junit] Running org.biojavax.EmptyRichAnnotationTest - [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec [junit] Running org.biojavax.SimpleCommentTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 sec [junit] Running org.biojavax.SimpleCrossRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.036 sec [junit] Running org.biojavax.SimpleDocRefAuthorTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 sec [junit] Running org.biojavax.SimpleDocRefTest - [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.015 sec [junit] Running org.biojavax.SimpleNamespaceTest - [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 13, Failures: 2, Errors: 1, Skipped: 0, Time elapsed: 0.014 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 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.SimpleRankedCrossRefTest - [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 sec [junit] Running org.biojavax.SimpleRankedDocRefTest - [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 sec + [junit] Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.SimpleRichAnnotationTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.bio.SimpleBioEntryTest - [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 32, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 0.025 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: 0.003 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.bio.seq.MultiSourceCompoundRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.bio.seq.SimpleRichFeatureTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.004 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.025 sec [junit] Running org.biojavax.bio.seq.SimpleRichLocationTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.bio.seq.io.Bug2249_2248Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.078 sec [junit] Running org.biojavax.bio.seq.io.Bug2250_2256Test - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.126 sec [junit] Running org.biojavax.bio.seq.io.Bug2255Test - [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: 0.02 sec [junit] Running org.biojavax.bio.seq.io.EMBLFormatTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 sec [junit] Running org.biojavax.bio.seq.io.GenbankFormatTest - [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec + [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.043 sec [junit] Running org.biojavax.bio.seq.io.INSDseqFormatTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.042 sec [junit] Running org.biojavax.bio.seq.io.UniProtFormatTest - [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: 0.032 sec [junit] Running org.biojavax.bio.taxa.SimpleNCBITaxonNameTest - [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.ga.functions.ProportionalSelectionTest - [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: 0.028 sec [junit] Running org.biojavax.ga.functions.SimpleCrossOverFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.011 sec [junit] Running org.biojavax.ga.functions.SimpleMutationFunctionTest - [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.012 sec [junit] Running org.biojavax.ga.impl.SimpleOrganismTest - [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.ga.impl.SimplePopulationTest - [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.ga.util.GAToolsTest - [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 sec [junit] Running org.biojavax.ga.util.WeightedSetTest - [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.ontology.SimpleComparableOntologyTest - [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 sec + [junit] Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.018 sec [junit] Running org.biojavax.ontology.SimpleComparableTermTest - [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 sec + [junit] Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec [junit] Running org.biojavax.ontology.SimpleComparableTripleTest - [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec + [junit] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.009 sec BUILD SUCCESSFUL -Total time: 17 seconds +Total time: 41 seconds make[1]: Leaving directory '/build/biojava-live-1.7.1' dh_installdocs dh_installchangelogs @@ -2103,21 +2147,23 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libbiojava-java-demos' in '../libbiojava-java-demos_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-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-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biojava-live_1.7.1-8_i386.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/26242/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26242/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/50716 and its subdirectories -I: Current time: Sun Jul 26 06:45:35 -12 2020 -I: pbuilder-time-stamp: 1595789135 +I: removing directory /srv/workspace/pbuilder/26242 and its subdirectories +I: Current time: Tue Jun 25 03:04:38 +14 2019 +I: pbuilder-time-stamp: 1561381478