simple 04-Oct-2024 21:47:51 Build Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job #2 (JB-GDL30-JOB1-2) started building on agent Default Agent simple 04-Oct-2024 21:47:51 simple 04-Oct-2024 21:47:51 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1 simple 04-Oct-2024 21:47:51 Executing build Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job #2 (JB-GDL30-JOB1-2) simple 04-Oct-2024 21:47:51 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 04-Oct-2024 21:47:51 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1 simple 04-Oct-2024 21:47:51 Updating source code to revision: 9e54c643f2bcf3e3c22685e6fadaa28e470fd97a simple 04-Oct-2024 21:47:51 Fetching 'refs/heads/improvement/JAL-4469_handling_uniprot_versioned_accesion_ids' from 'http://source.jalview.org/git/jalview.git'. simple 04-Oct-2024 21:47:52 Checking out revision 9e54c643f2bcf3e3c22685e6fadaa28e470fd97a. simple 04-Oct-2024 21:47:52 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 04-Oct-2024 21:47:52 839b67d..9e54c64 improvement/JAL-4469_handling_uniprot_versioned_accesion_ids -> origin/improvement/JAL-4469_handling_uniprot_versioned_accesion_ids simple 04-Oct-2024 21:47:53 Already on 'improvement/JAL-4469_handling_uniprot_versioned_accesion_ids' simple 04-Oct-2024 21:47:53 Your branch is behind 'origin/improvement/JAL-4469_handling_uniprot_versioned_accesion_ids' by 1 commit, and can be fast-forwarded. simple 04-Oct-2024 21:47:53 (use "git pull" to update your local branch) simple 04-Oct-2024 21:47:53 HEAD is now at 9e54c64 JAL-4469 Added a checkbox to remove version numbers from accession ids enabled/visible only for selected dbs (currently only uniprot). Added some tests for expected query string manipulation. simple 04-Oct-2024 21:47:53 Updated source code to revision: 9e54c643f2bcf3e3c22685e6fadaa28e470fd97a simple 04-Oct-2024 21:47:53 Finished task 'Checkout Default Repository' with result: Success simple 04-Oct-2024 21:47:53 Running pre-build action: VCS Version Collector simple 04-Oct-2024 21:47:53 Running pre-build action: Artifactory Release Staging command 04-Oct-2024 21:47:53 Substituting variable: ${bamboo.planKey} with JB-GDL30 simple 04-Oct-2024 21:47:53 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 04-Oct-2024 21:47:53 Bamboo Artifactory Plugin version: 2.6.2 command 04-Oct-2024 21:47:53 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job #2 (JB-GDL30-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL30 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_dependency_parent_0=JB-GDB631-2\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_revision_number=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL30-JOB1-2\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_repository_46498126_git_username=\nbamboo_buildKey=JB-GDL30-JOB1\nbamboo_repository_46498126_revision_number=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_repository_46498126_git_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_shortPlanName=improvement-JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_buildNumber=2\nbamboo_repository_46498126_branch_name=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL30-JOB1-2\nbamboo_repository_46498126_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_shortPlanKey=GDL30\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_buildTimeStamp=2024-10-04T21:42:48.150+01:00\nbamboo_repository_previous_revision_number=839b67dfeae7dc17cc31bfd9035f70b22655995b\nbamboo_repository_git_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_buildResultKey=JB-GDL30-JOB1-2\nbamboo_repository_branch_name=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_46498126_name=Jalview Git\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_46498126_previous_revision_number=839b67dfeae7dc17cc31bfd9035f70b22655995b\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301851\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\nbamboo_planKey=JB-GDL30\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 04-Oct-2024 21:47:55 build 04-Oct-2024 21:47:55 > Configure project : build 04-Oct-2024 21:47:55 Using properties from file './utils/channels/default/channel_gradle.properties' build 04-Oct-2024 21:47:55 JALVIEW_VERSION is set to '2.11.4.0' build 04-Oct-2024 21:47:55 HEADLESS BUILD build 04-Oct-2024 21:47:55 J2S ENABLED build 04-Oct-2024 21:47:55 Using a BUILD profile. build 04-Oct-2024 21:47:55 eclipseDir exists build 04-Oct-2024 21:47:55 build 04-Oct-2024 21:47:55 > Task :clean build 04-Oct-2024 21:47:55 > Task :cleanPackageDir build 04-Oct-2024 21:47:55 > Task :getdownImagesCopy build 04-Oct-2024 21:47:55 > Task :getdownImagesProcess build 04-Oct-2024 21:47:55 > Task :getdownImages build 04-Oct-2024 21:47:55 > Task :copyHelp build 04-Oct-2024 21:47:56 > Task :buildIndices build 04-Oct-2024 21:47:56 > Task :copyResources build 04-Oct-2024 21:47:56 > Task :copyChannelResources build 04-Oct-2024 21:47:56 build 04-Oct-2024 21:47:56 > Task :createBuildProperties build 04-Oct-2024 21:47:56 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 04-Oct-2024 21:47:56 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:47:56 build 04-Oct-2024 21:47:56 > Task :buildResources build 04-Oct-2024 21:47:57 > Task :copyDocs build 04-Oct-2024 21:47:57 build 04-Oct-2024 21:47:57 > Task :convertMdFiles build 04-Oct-2024 21:47:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 04-Oct-2024 21:47:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build/doc/releaseprocess.html build 04-Oct-2024 21:47:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 04-Oct-2024 21:47:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build/doc/building.html build 04-Oct-2024 21:47:57 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build/doc/jalview-projects.html build 04-Oct-2024 21:47:57 build 04-Oct-2024 21:47:57 > Task :releasesTemplates build 04-Oct-2024 21:47:57 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 04-Oct-2024 21:47:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:47:57 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:47:57 Stripping rc/test/etc for 2_11_4_0 build 04-Oct-2024 21:47:57 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md build 04-Oct-2024 21:47:57 build 04-Oct-2024 21:47:57 > Task :prepare build 04-Oct-2024 21:47:59 build 04-Oct-2024 21:47:59 > Task :compileJava build 04-Oct-2024 21:47:59 Setting target compatibility to 11 error 04-Oct-2024 21:48:05 Note: Some input files use or override a deprecated API. error 04-Oct-2024 21:48:05 Note: Recompile with -Xlint:deprecation for details. error 04-Oct-2024 21:48:05 Note: Some input files use unchecked or unsafe operations. error 04-Oct-2024 21:48:05 Note: Recompile with -Xlint:unchecked for details. build 04-Oct-2024 21:48:05 build 04-Oct-2024 21:48:05 > Task :processResources build 04-Oct-2024 21:48:05 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:05 build 04-Oct-2024 21:48:05 > Task :classes build 04-Oct-2024 21:48:06 build 04-Oct-2024 21:48:06 > Task :compileLinkCheck build 04-Oct-2024 21:48:06 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 04-Oct-2024 21:48:06 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:06 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:06 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 04-Oct-2024 21:48:08 build 04-Oct-2024 21:48:08 > Task :linkCheck build 04-Oct-2024 21:48:08 Checking help file links build 04-Oct-2024 21:50:14 build 04-Oct-2024 21:50:14 Results: build 04-Oct-2024 21:50:14 159 distinct help targets build 04-Oct-2024 21:50:14 159 help mappings build 04-Oct-2024 21:50:14 0 invalid targets build 04-Oct-2024 21:50:14 32 unused targets build 04-Oct-2024 21:50:14 uniprotfetcher: html/features/uniprotsequencefetcher.html build 04-Oct-2024 21:50:14 overviewprefs: html/features/preferences.html#overview build 04-Oct-2024 21:50:14 cdnafeatures: html/features/codingfeatures.html build 04-Oct-2024 21:50:14 startupprefs: html/features/preferences.html#startup build 04-Oct-2024 21:50:14 ensemblfetch: html/features/ensemblsequencefetcher.html build 04-Oct-2024 21:50:14 io.modellerpir: html/io/modellerpir.html build 04-Oct-2024 21:50:14 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 04-Oct-2024 21:50:14 pdbmcviewer: html/features/pdbviewer.html build 04-Oct-2024 21:50:14 workingwithpae: html/features/paematrices.html build 04-Oct-2024 21:50:14 groovy.colours: html/features/groovy.html#groovyColours build 04-Oct-2024 21:50:14 seqmappings: html/features/seqmappings.html build 04-Oct-2024 21:50:14 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 04-Oct-2024 21:50:14 splitframe.mirrorfonts: html/features/splitView.html#mirror build 04-Oct-2024 21:50:14 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 04-Oct-2024 21:50:14 search: html/features/search.html build 04-Oct-2024 21:50:14 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 04-Oct-2024 21:50:14 alformats: html/io/fileformats.html build 04-Oct-2024 21:50:14 strucprefs: html/features/preferences.html#structure build 04-Oct-2024 21:50:14 siftsmapping: html/features/siftsmapping.html build 04-Oct-2024 21:50:14 chimera.annotxfer: html/features/chimera.html#annotxfer build 04-Oct-2024 21:50:14 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 04-Oct-2024 21:50:14 newkeys: html/features/newkeystrokes.html build 04-Oct-2024 21:50:14 importvcf.attribs: html/features/importvcf.html#attribs build 04-Oct-2024 21:50:14 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 04-Oct-2024 21:50:14 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 04-Oct-2024 21:50:14 jalarchive: html/features/jalarchive.html build 04-Oct-2024 21:50:14 newsreader: html/webServices/newsreader.html build 04-Oct-2024 21:50:14 jalviewcltool: html/features/commandline.html#script build 04-Oct-2024 21:50:14 popMenuAddref: html/menus/popupMenu.html#addrefannot build 04-Oct-2024 21:50:14 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 04-Oct-2024 21:50:14 paematrixformat: html/io/paematrixformat.html build 04-Oct-2024 21:50:14 overview: html/features/overview.html build 04-Oct-2024 21:50:14 0 invalid map urls build 04-Oct-2024 21:50:14 0 invalid image attributes build 04-Oct-2024 21:50:14 508 internal href links (110 with anchors) build 04-Oct-2024 21:50:14 0 invalid internal href links build 04-Oct-2024 21:50:14 0 invalid internal anchor links build 04-Oct-2024 21:50:14 113 external href links build 04-Oct-2024 21:50:14 External links not verified as internet not available build 04-Oct-2024 21:50:14 *** Success *** build 04-Oct-2024 21:50:15 build 04-Oct-2024 21:50:15 > Task :jar build 04-Oct-2024 21:50:15 > Task :syncJars build 04-Oct-2024 21:50:15 > Task :makeDist build 04-Oct-2024 21:50:16 > Task :getdownWebsiteBuild build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 > Task :getdownDigest build 04-Oct-2024 21:50:17 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 04-Oct-2024 21:50:17 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 > Task :getdown build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 04-Oct-2024 21:50:17 Please consult deprecation warnings for more details. build 04-Oct-2024 21:50:17 build 04-Oct-2024 21:50:17 BUILD SUCCESSFUL in 2m 23s build 04-Oct-2024 21:50:17 21 actionable tasks: 21 executed error 04-Oct-2024 21:50:17 2024/10/04 21:50:16:418 WARNING Starting without install4j classes error 04-Oct-2024 21:50:17 2024/10/04 21:50:17:025 WARNING Starting without install4j classes simple 04-Oct-2024 21:50:18 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 04-Oct-2024 21:50:18 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 04-Oct-2024 21:50:18 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job #2 (JB-GDL30-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL30-JOB1-2-ScriptBuildTask-8778971055657397439.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_dependency_parent_0=JB-GDB631-2\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_revision_number=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL30-JOB1-2\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_repository_46498126_git_username=\nbamboo_buildKey=JB-GDL30-JOB1\nbamboo_repository_46498126_revision_number=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_repository_46498126_git_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_shortPlanName=improvement-JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_planRepository_name=Jalview Git\nbamboo_buildNumber=2\nbamboo_repository_46498126_branch_name=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL30-JOB1-2\nbamboo_repository_46498126_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_shortPlanKey=GDL30\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_buildTimeStamp=2024-10-04T21:42:48.150+01:00\nbamboo_repository_previous_revision_number=839b67dfeae7dc17cc31bfd9035f70b22655995b\nbamboo_repository_git_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_buildResultKey=JB-GDL30-JOB1-2\nbamboo_repository_branch_name=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - improvement-JAL-4469_handling_uniprot_versioned_accesion_ids - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=9e54c643f2bcf3e3c22685e6fadaa28e470fd97a\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Git\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL30 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_46498126_name=Jalview Git\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\nbamboo_repository_46498126_previous_revision_number=839b67dfeae7dc17cc31bfd9035f70b22655995b\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46301851\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL30-JOB1\nbamboo_planKey=JB-GDL30\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=improvement/JAL-4469_handling_uniprot_versioned_accesion_ids\n simple 04-Oct-2024 21:50:18 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 04-Oct-2024 21:50:18 Running post build plugin 'NCover Results Collector' simple 04-Oct-2024 21:50:18 Running post build plugin 'Artifact Copier' simple 04-Oct-2024 21:50:18 Publishing an artifact: getdown simple 04-Oct-2024 21:50:18 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 95.01 ms simple 04-Oct-2024 21:50:18 Running post build plugin 'Artifactory Release Management Staging' simple 04-Oct-2024 21:50:18 Running post build plugin 'Artifactory Build Info Copier' simple 04-Oct-2024 21:50:18 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 04-Oct-2024 21:50:18 Running post build plugin 'npm Cache Cleanup' simple 04-Oct-2024 21:50:18 Running post build plugin 'Clover Results Collector' simple 04-Oct-2024 21:50:18 Running post build plugin 'Docker Container Cleanup' simple 04-Oct-2024 21:50:18 Finalising the build... simple 04-Oct-2024 21:50:18 Stopping timer. simple 04-Oct-2024 21:50:18 Build JB-GDL30-JOB1-2 completed. simple 04-Oct-2024 21:50:18 Running on server: post build plugin 'NCover Results Collector' simple 04-Oct-2024 21:50:18 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 04-Oct-2024 21:50:18 Running on server: post build plugin 'Clover Delta Calculator' simple 04-Oct-2024 21:50:18 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 04-Oct-2024 21:50:18 All post build plugins have finished simple 04-Oct-2024 21:50:18 Generating build results summary... simple 04-Oct-2024 21:50:18 Saving build results to disk... simple 04-Oct-2024 21:50:18 Logging substituted variables... simple 04-Oct-2024 21:50:18 Indexing build results... simple 04-Oct-2024 21:50:18 Finished building JB-GDL30-JOB1-2.