simple 07-Jul-2020 01:59:22 Build Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #4 (JB-JGP14-JOB1-4) started building on agent Default Agent simple 07-Jul-2020 01:59:22 simple 07-Jul-2020 01:59:22 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1 simple 07-Jul-2020 01:59:22 Executing build Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #4 (JB-JGP14-JOB1-4) simple 07-Jul-2020 01:59:22 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 07-Jul-2020 01:59:22 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1 simple 07-Jul-2020 01:59:22 Updating source code to revision: 3db640482c218a4cc8919189fef1842424a0b9fd simple 07-Jul-2020 01:59:22 Fetching 'refs/heads/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' from 'http://source.jalview.org/git/jalview.git'. simple 07-Jul-2020 01:59:23 Checking out revision 3db640482c218a4cc8919189fef1842424a0b9fd. simple 07-Jul-2020 01:59:25 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 07-Jul-2020 01:59:25 06d91fe..3db6404 bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows -> origin/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows simple 07-Jul-2020 01:59:25 * [new tag] Release_2_10_2b1 -> Release_2_10_2b1 simple 07-Jul-2020 01:59:25 * [new tag] Release_2_10_2b2 -> Release_2_10_2b2 simple 07-Jul-2020 01:59:25 * [new tag] Release_2_10_3 -> Release_2_10_3 simple 07-Jul-2020 01:59:25 * [new tag] Release_2_10_4b1 -> Release_2_10_4b1 simple 07-Jul-2020 01:59:25 * [new tag] Release_2_11_0 -> Release_2_11_0 simple 07-Jul-2020 01:59:25 Already on 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' simple 07-Jul-2020 01:59:25 Your branch is behind 'origin/bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' by 35 commits, and can be fast-forwarded. simple 07-Jul-2020 01:59:25 (use "git pull" to update your local branch) simple 07-Jul-2020 01:59:25 HEAD is now at 3db6404 JAL-3685 Fixed single quotes in formatMessage messages simple 07-Jul-2020 01:59:25 Updated source code to revision: 3db640482c218a4cc8919189fef1842424a0b9fd simple 07-Jul-2020 01:59:25 Finished task 'Checkout Default Repository' with result: Success simple 07-Jul-2020 01:59:25 Running pre-build action: VCS Version Collector simple 07-Jul-2020 01:59:25 Running pre-build action: Artifactory Release Staging command 07-Jul-2020 01:59:25 Substituting variable: ${bamboo.planKey} with JB-JGP14 simple 07-Jul-2020 01:59:25 Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Jul-2020 01:59:25 Bamboo Artifactory Plugin version: 2.6.2 command 07-Jul-2020 01:59:25 Beginning to execute external process for build 'Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #4 (JB-JGP14-JOB1-4)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PJAVA_VERSION=11 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP14 clean makeDist shadowJar getdown installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\n ... using extra environment variables: 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build 07-Jul-2020 01:59:28 build 07-Jul-2020 01:59:28 > Configure project : build 07-Jul-2020 01:59:28 HEADLESS BUILD build 07-Jul-2020 01:59:28 Using a BUILD profile. build 07-Jul-2020 01:59:28 build 07-Jul-2020 01:59:28 > Task :clean build 07-Jul-2020 01:59:28 > Task :cleanPackageDir build 07-Jul-2020 01:59:29 > Task :copyHelp build 07-Jul-2020 01:59:30 > Task :buildIndices build 07-Jul-2020 01:59:32 build 07-Jul-2020 01:59:32 > Task :compileJava build 07-Jul-2020 01:59:32 Setting target compatibility to 11 error 07-Jul-2020 01:59:37 Note: Some input files use or override a deprecated API. error 07-Jul-2020 01:59:37 Note: Recompile with -Xlint:deprecation for details. error 07-Jul-2020 01:59:37 Note: Some input files use unchecked or unsafe operations. error 07-Jul-2020 01:59:37 Note: Recompile with -Xlint:unchecked for details. build 07-Jul-2020 01:59:37 build 07-Jul-2020 01:59:37 > Task :processResources build 07-Jul-2020 01:59:37 > Task :classes build 07-Jul-2020 01:59:37 > Task :setGitVals UP-TO-DATE build 07-Jul-2020 01:59:37 > Task :createBuildProperties build 07-Jul-2020 01:59:39 > Task :compileLinkCheck build 07-Jul-2020 01:59:39 > Task :cleanBuildingHTML UP-TO-DATE build 07-Jul-2020 01:59:39 > Task :convertBuildingMD build 07-Jul-2020 01:59:39 > Task :syncDocs build 07-Jul-2020 01:59:39 > Task :syncResources build 07-Jul-2020 01:59:39 > Task :prepare build 07-Jul-2020 01:59:40 build 07-Jul-2020 01:59:40 > Task :linkCheck build 07-Jul-2020 01:59:40 Checking help file links build 07-Jul-2020 01:59:40 build 07-Jul-2020 01:59:40 Results: build 07-Jul-2020 01:59:40 138 distinct help targets build 07-Jul-2020 01:59:40 138 help mappings build 07-Jul-2020 01:59:40 0 invalid targets build 07-Jul-2020 01:59:40 24 unused targets build 07-Jul-2020 01:59:40 uniprotfetcher: html/features/uniprotsequencefetcher.html build 07-Jul-2020 01:59:40 overviewprefs: html/features/preferences.html#overview build 07-Jul-2020 01:59:40 cdnafeatures: html/features/codingfeatures.html build 07-Jul-2020 01:59:40 ensemblfetch: html/features/ensemblsequencefetcher.html build 07-Jul-2020 01:59:40 io.modellerpir: html/io/modellerpir.html build 07-Jul-2020 01:59:40 pdbmcviewer: html/features/pdbviewer.html build 07-Jul-2020 01:59:40 groovy.colours: html/features/groovy.html#groovyColours build 07-Jul-2020 01:59:40 seqmappings: html/features/seqmappings.html build 07-Jul-2020 01:59:40 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 07-Jul-2020 01:59:40 splitframe.mirrorfonts: html/features/splitView.html#mirror build 07-Jul-2020 01:59:40 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 07-Jul-2020 01:59:40 search: html/features/search.html build 07-Jul-2020 01:59:40 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 07-Jul-2020 01:59:40 alformats: html/io/fileformats.html build 07-Jul-2020 01:59:40 strucprefs: html/features/preferences.html#structure build 07-Jul-2020 01:59:40 siftsmapping: html/features/siftsmapping.html build 07-Jul-2020 01:59:40 chimera.annotxfer: html/features/chimera.html#annotxfer build 07-Jul-2020 01:59:40 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 07-Jul-2020 01:59:40 newkeys: html/features/newkeystrokes.html build 07-Jul-2020 01:59:40 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 07-Jul-2020 01:59:40 jalarchive: html/features/jalarchive.html build 07-Jul-2020 01:59:40 newsreader: html/webServices/newsreader.html build 07-Jul-2020 01:59:40 popMenuAddref: html/menus/popupMenu.html#addrefannot build 07-Jul-2020 01:59:40 overview: html/features/overview.html build 07-Jul-2020 01:59:40 0 invalid map urls build 07-Jul-2020 01:59:40 0 invalid image attributes build 07-Jul-2020 01:59:40 386 internal href links (74 with anchors) build 07-Jul-2020 01:59:40 0 invalid internal href links build 07-Jul-2020 01:59:40 0 invalid internal anchor links build 07-Jul-2020 01:59:40 87 external href links build 07-Jul-2020 01:59:40 External links not verified as internet not available build 07-Jul-2020 01:59:40 *** Success *** build 07-Jul-2020 01:59:41 build 07-Jul-2020 01:59:41 > Task :jar build 07-Jul-2020 01:59:41 > Task :syncJars build 07-Jul-2020 01:59:41 > Task :makeDist build 07-Jul-2020 01:59:49 > Task :shadowJar build 07-Jul-2020 01:59:49 > Task :getdownWebsite build 07-Jul-2020 01:59:50 build 07-Jul-2020 01:59:50 > Task :getdownDigest build 07-Jul-2020 01:59:50 Generating digest file './getdown/website/11/digest.txt'... build 07-Jul-2020 01:59:50 Generating digest file './getdown/website/11/digest2.txt'... build 07-Jul-2020 01:59:50 build 07-Jul-2020 01:59:50 > Task :getdown error 07-Jul-2020 01:59:50 2020/07/07 01:59:49:693 WARNING Starting without install4j classes error 07-Jul-2020 01:59:50 2020/07/07 01:59:50:195 WARNING Starting without install4j classes build 07-Jul-2020 01:59:51 > Task :copyInstall4jTemplate build 07-Jul-2020 01:59:53 build 07-Jul-2020 01:59:53 > Task :installers build 07-Jul-2020 01:59:53 Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j build 07-Jul-2020 01:59:54 install4j version 8.0.5 (build 8155), built on 2020-03-16 build 07-Jul-2020 01:59:54 Using Java 1.8.0_252 from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64/jre build 07-Jul-2020 01:59:54 Registered to Jalview, University of Dundee build 07-Jul-2020 01:59:54 build 07-Jul-2020 01:59:54 Loading config file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j build 07-Jul-2020 01:59:56 Creating media file 'Windows x64 EXE Installer': build 07-Jul-2020 01:59:56 Collecting files: build 07-Jul-2020 01:59:56 [WARNING] The version of the bundled JRE is too low. It should be at least 11! build 07-Jul-2020 01:59:56 Compiling launchers: build 07-Jul-2020 01:59:56 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 01:59:56 Generating VM options file jalview.vmoptions. build 07-Jul-2020 01:59:56 Creating media file: build 07-Jul-2020 01:59:56 Using custom installer icon: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/../../resources/images/jalview_logos.ico build 07-Jul-2020 01:59:58 Zipping custom code & resources JAR file build 07-Jul-2020 01:59:58 Identifying components build 07-Jul-2020 01:59:58 Adding JRE (jre-11-windows-x64.tar.gz) build 07-Jul-2020 01:59:58 Shrinking runtime build 07-Jul-2020 01:59:58 build 07-Jul-2020 01:59:58 Creating media file 'macOS Disk Image': build 07-Jul-2020 01:59:58 Collecting files: build 07-Jul-2020 01:59:58 Compiling launchers: build 07-Jul-2020 01:59:58 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 01:59:58 Generating VM options file vmoptions.txt. build 07-Jul-2020 01:59:58 Creating media file: build 07-Jul-2020 01:59:58 Identifying components build 07-Jul-2020 01:59:59 Shrinking runtime build 07-Jul-2020 01:59:59 build 07-Jul-2020 01:59:59 Creating media file 'Linux x64 Shell Installer': build 07-Jul-2020 01:59:59 Collecting files: build 07-Jul-2020 01:59:59 [WARNING] The version of the bundled JRE is too low. It should be at least 11! build 07-Jul-2020 01:59:59 Compiling launchers: build 07-Jul-2020 01:59:59 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 01:59:59 Generating launcher script file build 07-Jul-2020 01:59:59 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 01:59:59 Creating media file: build 07-Jul-2020 01:59:59 Generating launcher script file build 07-Jul-2020 02:00:00 Zipping custom code & resources JAR file build 07-Jul-2020 02:00:00 Identifying components build 07-Jul-2020 02:00:00 Adding JRE (jre-11-linux-x64.tar.gz) build 07-Jul-2020 02:00:00 Shrinking runtime build 07-Jul-2020 02:00:00 build 07-Jul-2020 02:00:00 Creating media file 'Unix .tar.gz Archive': build 07-Jul-2020 02:00:00 Collecting files: build 07-Jul-2020 02:00:00 Compiling launchers: build 07-Jul-2020 02:00:00 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:00 Generating launcher script file build 07-Jul-2020 02:00:00 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 02:00:00 Creating media file: build 07-Jul-2020 02:00:00 Identifying components build 07-Jul-2020 02:00:01 Shrinking runtime build 07-Jul-2020 02:00:01 build 07-Jul-2020 02:00:01 Creating media file 'Unix Shell Installer': build 07-Jul-2020 02:00:01 Collecting files: build 07-Jul-2020 02:00:01 Compiling launchers: build 07-Jul-2020 02:00:01 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:01 Generating launcher script file build 07-Jul-2020 02:00:01 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 02:00:01 Creating media file: build 07-Jul-2020 02:00:01 Generating launcher script file build 07-Jul-2020 02:00:02 Zipping custom code & resources JAR file build 07-Jul-2020 02:00:02 Identifying components build 07-Jul-2020 02:00:02 Shrinking runtime build 07-Jul-2020 02:00:02 build 07-Jul-2020 02:00:02 Compressing 5 media files with 4 threads: build 07-Jul-2020 02:00:18 build 07-Jul-2020 02:00:18 Compressed media file 'macOS Disk Image': build 07-Jul-2020 02:00:18 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11 build 07-Jul-2020 02:00:18 The name of the media file is Jalview_Build-2_11_1_0-macos-java_11.dmg. build 07-Jul-2020 02:00:18 The size of the media file is 82.0 MB build 07-Jul-2020 02:00:21 build 07-Jul-2020 02:00:21 Compressed media file 'Unix .tar.gz Archive': build 07-Jul-2020 02:00:21 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11 build 07-Jul-2020 02:00:21 The name of the media file is jalview_build-2_11_1_0-unix-java_11.tar.gz. build 07-Jul-2020 02:00:21 The size of the media file is 44.7 MB build 07-Jul-2020 02:00:27 build 07-Jul-2020 02:00:27 Compressed media file 'Unix Shell Installer': build 07-Jul-2020 02:00:27 Compressing files build 07-Jul-2020 02:00:27 Applying LZMA compression build 07-Jul-2020 02:00:27 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11 build 07-Jul-2020 02:00:27 The name of the media file is jalview_build-2_11_1_0-unix-java_11.sh. build 07-Jul-2020 02:00:27 The size of the media file is 40.1 MB build 07-Jul-2020 02:00:29 build 07-Jul-2020 02:00:29 Compressed media file 'Windows x64 EXE Installer': build 07-Jul-2020 02:00:29 Compressing files build 07-Jul-2020 02:00:29 Applying LZMA compression build 07-Jul-2020 02:00:29 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11 build 07-Jul-2020 02:00:29 The name of the media file is Jalview_Build-2_11_1_0-windows-x64-java_11.exe. build 07-Jul-2020 02:00:29 The size of the media file is 81.0 MB build 07-Jul-2020 02:00:29 build 07-Jul-2020 02:00:29 Compressed media file 'Linux x64 Shell Installer': build 07-Jul-2020 02:00:29 Compressing files build 07-Jul-2020 02:00:29 Applying LZMA compression build 07-Jul-2020 02:00:29 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/11 build 07-Jul-2020 02:00:29 The name of the media file is jalview_build-2_11_1_0-linux_x64-java_11.sh. build 07-Jul-2020 02:00:29 The size of the media file is 79.8 MB build 07-Jul-2020 02:00:29 Writing md5sums. build 07-Jul-2020 02:00:29 Writing sha256sums. build 07-Jul-2020 02:00:29 Writing updates.xml. build 07-Jul-2020 02:00:29 Please upload updates.xml to https://www.jalview.org/install4j/updates.xml build 07-Jul-2020 02:00:29 and upload all generated media files to the same directory. build 07-Jul-2020 02:00:29 build 07-Jul-2020 02:00:29 Build completed in 34.8 seconds. build 07-Jul-2020 02:00:30 build 07-Jul-2020 02:00:30 BUILD SUCCESSFUL in 1m 5s build 07-Jul-2020 02:00:30 21 actionable tasks: 20 executed, 1 up-to-date simple 07-Jul-2020 02:00:31 Finished task 'Jalview distribution for Java 11' with result: Success command 07-Jul-2020 02:00:31 Substituting variable: ${bamboo.planKey} with JB-JGP14 simple 07-Jul-2020 02:00:31 Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 07-Jul-2020 02:00:31 Bamboo Artifactory Plugin version: 2.6.2 command 07-Jul-2020 02:00:31 Beginning to execute external process for build 'Jalview Builds - Gradle build with getdown and install4j - bug-JAL-3628_Unable_to_save_update_to_existing_file_in_Windows - Default Job #4 (JB-JGP14-JOB1-4)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PJAVA_VERSION=1.8 -PCHANNEL=BUILD -Pbamboo_planKey=JB-JGP14 shadowJar getdown installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1\n ... using extra environment variables: 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build 07-Jul-2020 02:00:32 build 07-Jul-2020 02:00:32 > Configure project : build 07-Jul-2020 02:00:32 HEADLESS BUILD build 07-Jul-2020 02:00:32 Using a BUILD profile. build 07-Jul-2020 02:00:34 build 07-Jul-2020 02:00:34 > Task :compileJava build 07-Jul-2020 02:00:34 Setting target compatibility to 1.8 error 07-Jul-2020 02:00:38 Note: Some input files use or override a deprecated API. error 07-Jul-2020 02:00:38 Note: Recompile with -Xlint:deprecation for details. error 07-Jul-2020 02:00:38 Note: Some input files use unchecked or unsafe operations. error 07-Jul-2020 02:00:38 Note: Recompile with -Xlint:unchecked for details. build 07-Jul-2020 02:00:38 build 07-Jul-2020 02:00:38 > Task :processResources UP-TO-DATE build 07-Jul-2020 02:00:38 > Task :classes build 07-Jul-2020 02:00:38 > Task :cleanPackageDir build 07-Jul-2020 02:00:38 > Task :copyHelp UP-TO-DATE build 07-Jul-2020 02:00:40 > Task :buildIndices build 07-Jul-2020 02:00:40 > Task :setGitVals UP-TO-DATE build 07-Jul-2020 02:00:40 > Task :createBuildProperties build 07-Jul-2020 02:00:41 > Task :compileLinkCheck build 07-Jul-2020 02:00:41 > Task :cleanBuildingHTML build 07-Jul-2020 02:00:41 > Task :convertBuildingMD build 07-Jul-2020 02:00:41 > Task :syncDocs UP-TO-DATE build 07-Jul-2020 02:00:41 > Task :syncResources UP-TO-DATE build 07-Jul-2020 02:00:41 > Task :prepare UP-TO-DATE build 07-Jul-2020 02:00:42 build 07-Jul-2020 02:00:42 > Task :linkCheck build 07-Jul-2020 02:00:42 Checking help file links build 07-Jul-2020 02:00:42 build 07-Jul-2020 02:00:42 Results: build 07-Jul-2020 02:00:42 138 distinct help targets build 07-Jul-2020 02:00:42 138 help mappings build 07-Jul-2020 02:00:42 0 invalid targets build 07-Jul-2020 02:00:42 24 unused targets build 07-Jul-2020 02:00:42 uniprotfetcher: html/features/uniprotsequencefetcher.html build 07-Jul-2020 02:00:42 overviewprefs: html/features/preferences.html#overview build 07-Jul-2020 02:00:42 cdnafeatures: html/features/codingfeatures.html build 07-Jul-2020 02:00:42 ensemblfetch: html/features/ensemblsequencefetcher.html build 07-Jul-2020 02:00:42 io.modellerpir: html/io/modellerpir.html build 07-Jul-2020 02:00:42 pdbmcviewer: html/features/pdbviewer.html build 07-Jul-2020 02:00:42 groovy.colours: html/features/groovy.html#groovyColours build 07-Jul-2020 02:00:42 seqmappings: html/features/seqmappings.html build 07-Jul-2020 02:00:42 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 07-Jul-2020 02:00:42 splitframe.mirrorfonts: html/features/splitView.html#mirror build 07-Jul-2020 02:00:42 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 07-Jul-2020 02:00:42 search: html/features/search.html build 07-Jul-2020 02:00:42 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 07-Jul-2020 02:00:42 alformats: html/io/fileformats.html build 07-Jul-2020 02:00:42 strucprefs: html/features/preferences.html#structure build 07-Jul-2020 02:00:42 siftsmapping: html/features/siftsmapping.html build 07-Jul-2020 02:00:42 chimera.annotxfer: html/features/chimera.html#annotxfer build 07-Jul-2020 02:00:42 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 07-Jul-2020 02:00:42 newkeys: html/features/newkeystrokes.html build 07-Jul-2020 02:00:42 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 07-Jul-2020 02:00:42 jalarchive: html/features/jalarchive.html build 07-Jul-2020 02:00:42 newsreader: html/webServices/newsreader.html build 07-Jul-2020 02:00:42 popMenuAddref: html/menus/popupMenu.html#addrefannot build 07-Jul-2020 02:00:42 overview: html/features/overview.html build 07-Jul-2020 02:00:42 0 invalid map urls build 07-Jul-2020 02:00:42 0 invalid image attributes build 07-Jul-2020 02:00:42 386 internal href links (74 with anchors) build 07-Jul-2020 02:00:42 0 invalid internal href links build 07-Jul-2020 02:00:42 0 invalid internal anchor links build 07-Jul-2020 02:00:42 87 external href links build 07-Jul-2020 02:00:42 External links not verified as internet not available build 07-Jul-2020 02:00:42 *** Success *** build 07-Jul-2020 02:00:43 build 07-Jul-2020 02:00:43 > Task :jar build 07-Jul-2020 02:00:43 > Task :syncJars build 07-Jul-2020 02:00:43 > Task :makeDist build 07-Jul-2020 02:00:48 > Task :shadowJar build 07-Jul-2020 02:00:48 > Task :getdownWebsite error 07-Jul-2020 02:00:49 2020/07/07 02:00:48:977 WARNING Starting without install4j classes error 07-Jul-2020 02:00:49 2020/07/07 02:00:49:445 WARNING Starting without install4j classes build 07-Jul-2020 02:00:49 build 07-Jul-2020 02:00:49 > Task :getdownDigest build 07-Jul-2020 02:00:49 Generating digest file './getdown/website/1.8/digest.txt'... build 07-Jul-2020 02:00:49 Generating digest file './getdown/website/1.8/digest2.txt'... build 07-Jul-2020 02:00:49 build 07-Jul-2020 02:00:49 > Task :getdown build 07-Jul-2020 02:00:49 > Task :copyInstall4jTemplate UP-TO-DATE build 07-Jul-2020 02:00:51 build 07-Jul-2020 02:00:51 > Task :installers build 07-Jul-2020 02:00:51 Using projectFile /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j build 07-Jul-2020 02:00:51 install4j version 8.0.5 (build 8155), built on 2020-03-16 build 07-Jul-2020 02:00:51 Using Java 1.8.0_252 from /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-2.el7_8.x86_64/jre build 07-Jul-2020 02:00:51 Registered to Jalview, University of Dundee build 07-Jul-2020 02:00:51 build 07-Jul-2020 02:00:51 Loading config file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/jalview-install4j-conf.install4j build 07-Jul-2020 02:00:51 Creating media file 'Windows x64 EXE Installer': build 07-Jul-2020 02:00:51 Collecting files: build 07-Jul-2020 02:00:51 [WARNING] The version of the bundled JRE is too low. It should be at least 1.8! build 07-Jul-2020 02:00:51 Compiling launchers: build 07-Jul-2020 02:00:51 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:51 Generating VM options file jalview.vmoptions. build 07-Jul-2020 02:00:51 Creating media file: build 07-Jul-2020 02:00:51 Using custom installer icon: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/utils/install4j/../../resources/images/jalview_logos.ico build 07-Jul-2020 02:00:52 Zipping custom code & resources JAR file build 07-Jul-2020 02:00:52 Identifying components build 07-Jul-2020 02:00:52 Adding JRE (jre-8-windows-x64.tar.gz) build 07-Jul-2020 02:00:52 Shrinking runtime build 07-Jul-2020 02:00:53 build 07-Jul-2020 02:00:53 Creating media file 'macOS Disk Image': build 07-Jul-2020 02:00:53 Collecting files: build 07-Jul-2020 02:00:53 Compiling launchers: build 07-Jul-2020 02:00:53 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:53 Generating VM options file vmoptions.txt. build 07-Jul-2020 02:00:53 Creating media file: build 07-Jul-2020 02:00:53 Identifying components build 07-Jul-2020 02:00:54 Shrinking runtime build 07-Jul-2020 02:00:54 build 07-Jul-2020 02:00:54 Creating media file 'Linux x64 Shell Installer': build 07-Jul-2020 02:00:54 Collecting files: build 07-Jul-2020 02:00:54 [WARNING] The version of the bundled JRE is too low. It should be at least 1.8! build 07-Jul-2020 02:00:54 Compiling launchers: build 07-Jul-2020 02:00:54 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:54 Generating launcher script file build 07-Jul-2020 02:00:54 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 02:00:54 Creating media file: build 07-Jul-2020 02:00:54 Generating launcher script file build 07-Jul-2020 02:00:55 Zipping custom code & resources JAR file build 07-Jul-2020 02:00:55 Identifying components build 07-Jul-2020 02:00:55 Adding JRE (jre-8-linux-x64.tar.gz) build 07-Jul-2020 02:00:55 Shrinking runtime build 07-Jul-2020 02:00:55 build 07-Jul-2020 02:00:55 Creating media file 'Unix .tar.gz Archive': build 07-Jul-2020 02:00:55 Collecting files: build 07-Jul-2020 02:00:55 Compiling launchers: build 07-Jul-2020 02:00:55 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:55 Generating launcher script file build 07-Jul-2020 02:00:55 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 02:00:55 Creating media file: build 07-Jul-2020 02:00:55 Identifying components build 07-Jul-2020 02:00:56 Shrinking runtime build 07-Jul-2020 02:00:56 build 07-Jul-2020 02:00:56 Creating media file 'Unix Shell Installer': build 07-Jul-2020 02:00:56 Collecting files: build 07-Jul-2020 02:00:56 Compiling launchers: build 07-Jul-2020 02:00:56 Compiling launcher 'Jalview Launcher': build 07-Jul-2020 02:00:56 Generating launcher script file build 07-Jul-2020 02:00:56 Generating VM options file .i4j_external_735/jalview.vmoptions. build 07-Jul-2020 02:00:56 Creating media file: build 07-Jul-2020 02:00:56 Generating launcher script file build 07-Jul-2020 02:00:56 Zipping custom code & resources JAR file build 07-Jul-2020 02:00:56 Identifying components build 07-Jul-2020 02:00:56 Shrinking runtime build 07-Jul-2020 02:00:57 build 07-Jul-2020 02:00:57 Compressing 5 media files with 4 threads: build 07-Jul-2020 02:01:14 build 07-Jul-2020 02:01:14 Compressed media file 'macOS Disk Image': build 07-Jul-2020 02:01:14 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8 build 07-Jul-2020 02:01:14 The name of the media file is Jalview_Build-2_11_1_0-macos-java_8.dmg. build 07-Jul-2020 02:01:14 The size of the media file is 75.7 MB build 07-Jul-2020 02:01:17 build 07-Jul-2020 02:01:17 Compressed media file 'Unix .tar.gz Archive': build 07-Jul-2020 02:01:17 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8 build 07-Jul-2020 02:01:17 The name of the media file is jalview_build-2_11_1_0-unix-java_8.tar.gz. build 07-Jul-2020 02:01:17 The size of the media file is 38.4 MB build 07-Jul-2020 02:01:18 build 07-Jul-2020 02:01:18 Compressed media file 'Unix Shell Installer': build 07-Jul-2020 02:01:18 Compressing files build 07-Jul-2020 02:01:18 Applying LZMA compression build 07-Jul-2020 02:01:18 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8 build 07-Jul-2020 02:01:18 The name of the media file is jalview_build-2_11_1_0-unix-java_8.sh. build 07-Jul-2020 02:01:18 The size of the media file is 34.1 MB build 07-Jul-2020 02:01:20 build 07-Jul-2020 02:01:20 Compressed media file 'Windows x64 EXE Installer': build 07-Jul-2020 02:01:20 Compressing files build 07-Jul-2020 02:01:20 Applying LZMA compression build 07-Jul-2020 02:01:20 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8 build 07-Jul-2020 02:01:20 The name of the media file is Jalview_Build-2_11_1_0-windows-x64-java_8.exe. build 07-Jul-2020 02:01:20 The size of the media file is 71.6 MB build 07-Jul-2020 02:01:20 build 07-Jul-2020 02:01:20 Compressed media file 'Linux x64 Shell Installer': build 07-Jul-2020 02:01:20 Compressing files build 07-Jul-2020 02:01:20 Applying LZMA compression build 07-Jul-2020 02:01:20 Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-JGP14-JOB1/build/install4j/1.8 build 07-Jul-2020 02:01:20 The name of the media file is jalview_build-2_11_1_0-linux_x64-java_8.sh. build 07-Jul-2020 02:01:20 The size of the media file is 73.1 MB build 07-Jul-2020 02:01:20 Writing md5sums. build 07-Jul-2020 02:01:20 Writing sha256sums. build 07-Jul-2020 02:01:20 Writing updates.xml. build 07-Jul-2020 02:01:20 Please upload updates.xml to https://www.jalview.org/install4j/updates.xml build 07-Jul-2020 02:01:20 and upload all generated media files to the same directory. build 07-Jul-2020 02:01:20 build 07-Jul-2020 02:01:20 Build completed in 30.2 seconds. build 07-Jul-2020 02:01:21 build 07-Jul-2020 02:01:21 BUILD SUCCESSFUL in 50s build 07-Jul-2020 02:01:21 20 actionable tasks: 15 executed, 5 up-to-date simple 07-Jul-2020 02:01:22 Finished task 'Jalview distribution for Java 8' with result: Success simple 07-Jul-2020 02:01:22 Running post build plugin 'NCover Results Collector' simple 07-Jul-2020 02:01:22 Running post build plugin 'Artifact Copier' simple 07-Jul-2020 02:01:22 Publishing an artifact: Jalview getdown launcher simple 07-Jul-2020 02:01:22 Finished publishing of artifact Shared artifact: [Jalview getdown launcher], pattern: [**/*] anchored at: [getdown/files] in 22.94 ms simple 07-Jul-2020 02:01:22 Publishing an artifact: getdown-channel simple 07-Jul-2020 02:01:22 Finished publishing of artifact Shared artifact: [getdown-channel], pattern: [**/*] anchored at: [getdown/website] in 287.4 ms simple 07-Jul-2020 02:01:22 Publishing an artifact: install4j installers simple 07-Jul-2020 02:01:24 Finished publishing of artifact Shared artifact: [install4j installers], pattern: [**/*] anchored at: [build/install4j] in 1.842 s simple 07-Jul-2020 02:01:24 Publishing an artifact: Jalview executables simple 07-Jul-2020 02:01:24 Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 242.0 ms simple 07-Jul-2020 02:01:24 Running post build plugin 'Artifactory Release Management Staging' simple 07-Jul-2020 02:01:24 Running post build plugin 'Artifactory Build Info Copier' simple 07-Jul-2020 02:01:24 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 07-Jul-2020 02:01:24 Running post build plugin 'npm Cache Cleanup' simple 07-Jul-2020 02:01:24 Running post build plugin 'Clover Results Collector' simple 07-Jul-2020 02:01:24 Running post build plugin 'Docker Container Cleanup' simple 07-Jul-2020 02:01:24 Finalising the build... simple 07-Jul-2020 02:01:24 Stopping timer. simple 07-Jul-2020 02:01:24 Build JB-JGP14-JOB1-4 completed. simple 07-Jul-2020 02:01:24 Running on server: post build plugin 'NCover Results Collector' simple 07-Jul-2020 02:01:24 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 07-Jul-2020 02:01:24 Running on server: post build plugin 'Clover Delta Calculator' simple 07-Jul-2020 02:01:24 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 07-Jul-2020 02:01:24 All post build plugins have finished simple 07-Jul-2020 02:01:24 Generating build results summary... simple 07-Jul-2020 02:01:24 Saving build results to disk... simple 07-Jul-2020 02:01:24 Logging substituted variables... simple 07-Jul-2020 02:01:24 Indexing build results... simple 07-Jul-2020 02:01:24 Finished building JB-JGP14-JOB1-4.