simple 28-Nov-2024 18:20:31 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job #3 (JB-GDL46-JOB1-3) started building on agent Default Agent simple 28-Nov-2024 18:20:31 simple 28-Nov-2024 18:20:31 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1 simple 28-Nov-2024 18:20:31 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job #3 (JB-GDL46-JOB1-3) simple 28-Nov-2024 18:20:31 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 28-Nov-2024 18:20:31 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1 simple 28-Nov-2024 18:20:31 Updating source code to revision: 4aa30fa9dd69fe01111355dda8b970a6ad9fca4c simple 28-Nov-2024 18:20:31 Fetching 'refs/heads/bug/JAL-4492_gradle_build_not_excluding_classes' from 'http://source.jalview.org/git/jalview.git'. simple 28-Nov-2024 18:20:31 Checking out revision 4aa30fa9dd69fe01111355dda8b970a6ad9fca4c. simple 28-Nov-2024 18:20:31 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 28-Nov-2024 18:20:31 f1f306f..4aa30fa bug/JAL-4492_gradle_build_not_excluding_classes -> origin/bug/JAL-4492_gradle_build_not_excluding_classes simple 28-Nov-2024 18:20:31 Already on 'bug/JAL-4492_gradle_build_not_excluding_classes' simple 28-Nov-2024 18:20:31 Your branch is behind 'origin/bug/JAL-4492_gradle_build_not_excluding_classes' by 1 commit, and can be fast-forwarded. simple 28-Nov-2024 18:20:31 (use "git pull" to update your local branch) simple 28-Nov-2024 18:20:31 HEAD is now at 4aa30fa JAL-3907 Add Java21 compliance to the build and download_jdk/jre helpers simple 28-Nov-2024 18:20:31 Updated source code to revision: 4aa30fa9dd69fe01111355dda8b970a6ad9fca4c simple 28-Nov-2024 18:20:31 Finished task 'Checkout Default Repository' with result: Success simple 28-Nov-2024 18:20:31 Running pre-build action: VCS Version Collector simple 28-Nov-2024 18:20:31 Running pre-build action: Artifactory Release Staging command 28-Nov-2024 18:20:31 Substituting variable: ${bamboo.planKey} with JB-GDL46 simple 28-Nov-2024 18:20:31 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 28-Nov-2024 18:20:31 Bamboo Artifactory Plugin version: 2.6.2 command 28-Nov-2024 18:20:31 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job #3 (JB-GDL46-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL46 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_dependency_parent_0=JB-GDB648-4\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=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_revision_number=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL46-JOB1-3\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-GDL46-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL46-JOB1\nbamboo_shortPlanName=bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498225_previous_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_planRepository_name=Jalview Git\nLOGNAME=bamboo\nbamboo_repository_46498225_git_username=\nbamboo_buildNumber=3\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-GDL46-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_name=Jalview Git\nbamboo_shortPlanKey=GDL46\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_buildTimeStamp=2024-11-28T18:15:10.761Z\nbamboo_repository_previous_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_repository_46498225_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildResultKey=JB-GDL46-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\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_repository_46498225_revision_number=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_planRepository_branch=bug/JAL-4492_gradle_build_not_excluding_classes\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=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\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-46302049\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-GDL46-JOB1\nbamboo_planKey=JB-GDL46\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 28-Nov-2024 18:20:33 build 28-Nov-2024 18:20:33 > Configure project : build 28-Nov-2024 18:20:33 Using properties from file './utils/channels/default/channel_gradle.properties' build 28-Nov-2024 18:20:33 JALVIEW_VERSION is set to '2.11.4.2' build 28-Nov-2024 18:20:33 HEADLESS BUILD build 28-Nov-2024 18:20:33 J2S ENABLED build 28-Nov-2024 18:20:33 Using a BUILD profile. build 28-Nov-2024 18:20:33 eclipseDir exists build 28-Nov-2024 18:20:33 build 28-Nov-2024 18:20:33 > Task :clean build 28-Nov-2024 18:20:33 > Task :cleanPackageDir build 28-Nov-2024 18:20:33 > Task :getdownImagesCopy build 28-Nov-2024 18:20:33 > Task :getdownImagesProcess build 28-Nov-2024 18:20:33 > Task :getdownImages build 28-Nov-2024 18:20:33 > Task :copyHelp build 28-Nov-2024 18:20:34 > Task :buildIndices build 28-Nov-2024 18:20:35 > Task :copyResources build 28-Nov-2024 18:20:35 > Task :copyChannelResources build 28-Nov-2024 18:20:35 build 28-Nov-2024 18:20:35 > Task :createBuildProperties build 28-Nov-2024 18:20:35 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 28-Nov-2024 18:20:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:35 build 28-Nov-2024 18:20:35 > Task :buildResources build 28-Nov-2024 18:20:35 > Task :copyDocs build 28-Nov-2024 18:20:35 build 28-Nov-2024 18:20:35 > Task :convertMdFiles build 28-Nov-2024 18:20:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 28-Nov-2024 18:20:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/build/resources/doc_build/doc/releaseprocess.html build 28-Nov-2024 18:20:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 28-Nov-2024 18:20:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/build/resources/doc_build/doc/building.html build 28-Nov-2024 18:20:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/build/resources/doc_build/doc/jalview-projects.html build 28-Nov-2024 18:20:35 build 28-Nov-2024 18:20:35 > Task :releasesTemplates build 28-Nov-2024 18:20:35 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 28-Nov-2024 18:20:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:35 Stripping rc/test/etc for 2_11_4_2 build 28-Nov-2024 18:20:35 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md build 28-Nov-2024 18:20:35 build 28-Nov-2024 18:20:35 > Task :prepare build 28-Nov-2024 18:20:37 build 28-Nov-2024 18:20:37 > Task :compileJava build 28-Nov-2024 18:20:37 Setting target compatibility to 11 error 28-Nov-2024 18:20:42 Note: Some input files use or override a deprecated API. error 28-Nov-2024 18:20:42 Note: Recompile with -Xlint:deprecation for details. error 28-Nov-2024 18:20:42 Note: Some input files use unchecked or unsafe operations. error 28-Nov-2024 18:20:42 Note: Recompile with -Xlint:unchecked for details. build 28-Nov-2024 18:20:43 build 28-Nov-2024 18:20:43 > Task :processResources build 28-Nov-2024 18:20:43 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:43 build 28-Nov-2024 18:20:43 > Task :classes build 28-Nov-2024 18:20:44 build 28-Nov-2024 18:20:44 > Task :compileLinkCheck build 28-Nov-2024 18:20:44 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 28-Nov-2024 18:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:44 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-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 28-Nov-2024 18:20:46 build 28-Nov-2024 18:20:46 > Task :linkCheck build 28-Nov-2024 18:20:46 Checking help file links build 28-Nov-2024 18:22:52 build 28-Nov-2024 18:22:52 Results: build 28-Nov-2024 18:22:52 159 distinct help targets build 28-Nov-2024 18:22:52 159 help mappings build 28-Nov-2024 18:22:52 0 invalid targets build 28-Nov-2024 18:22:52 32 unused targets build 28-Nov-2024 18:22:52 uniprotfetcher: html/features/uniprotsequencefetcher.html build 28-Nov-2024 18:22:52 overviewprefs: html/features/preferences.html#overview build 28-Nov-2024 18:22:52 cdnafeatures: html/features/codingfeatures.html build 28-Nov-2024 18:22:52 startupprefs: html/features/preferences.html#startup build 28-Nov-2024 18:22:52 ensemblfetch: html/features/ensemblsequencefetcher.html build 28-Nov-2024 18:22:52 io.modellerpir: html/io/modellerpir.html build 28-Nov-2024 18:22:52 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 28-Nov-2024 18:22:52 pdbmcviewer: html/features/pdbviewer.html build 28-Nov-2024 18:22:52 workingwithpae: html/features/paematrices.html build 28-Nov-2024 18:22:52 groovy.colours: html/features/groovy.html#groovyColours build 28-Nov-2024 18:22:52 seqmappings: html/features/seqmappings.html build 28-Nov-2024 18:22:52 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 28-Nov-2024 18:22:52 splitframe.mirrorfonts: html/features/splitView.html#mirror build 28-Nov-2024 18:22:52 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 28-Nov-2024 18:22:52 search: html/features/search.html build 28-Nov-2024 18:22:52 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 28-Nov-2024 18:22:52 alformats: html/io/fileformats.html build 28-Nov-2024 18:22:52 strucprefs: html/features/preferences.html#structure build 28-Nov-2024 18:22:52 siftsmapping: html/features/siftsmapping.html build 28-Nov-2024 18:22:52 chimera.annotxfer: html/features/chimera.html#annotxfer build 28-Nov-2024 18:22:52 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 28-Nov-2024 18:22:52 newkeys: html/features/newkeystrokes.html build 28-Nov-2024 18:22:52 importvcf.attribs: html/features/importvcf.html#attribs build 28-Nov-2024 18:22:52 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 28-Nov-2024 18:22:52 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 28-Nov-2024 18:22:52 jalarchive: html/features/jalarchive.html build 28-Nov-2024 18:22:52 newsreader: html/webServices/newsreader.html build 28-Nov-2024 18:22:52 jalviewcltool: html/features/commandline.html#script build 28-Nov-2024 18:22:52 popMenuAddref: html/menus/popupMenu.html#addrefannot build 28-Nov-2024 18:22:52 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 28-Nov-2024 18:22:52 paematrixformat: html/io/paematrixformat.html build 28-Nov-2024 18:22:52 overview: html/features/overview.html build 28-Nov-2024 18:22:52 0 invalid map urls build 28-Nov-2024 18:22:52 0 invalid image attributes build 28-Nov-2024 18:22:52 506 internal href links (110 with anchors) build 28-Nov-2024 18:22:52 0 invalid internal href links build 28-Nov-2024 18:22:52 0 invalid internal anchor links build 28-Nov-2024 18:22:52 112 external href links build 28-Nov-2024 18:22:52 External links not verified as internet not available build 28-Nov-2024 18:22:52 *** Success *** build 28-Nov-2024 18:22:53 build 28-Nov-2024 18:22:53 > Task :jar build 28-Nov-2024 18:22:53 > Task :syncJars build 28-Nov-2024 18:22:53 > Task :makeDist build 28-Nov-2024 18:22:53 > Task :getdownWebsiteBuild build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 > Task :getdownDigest build 28-Nov-2024 18:22:55 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 28-Nov-2024 18:22:55 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 > Task :getdown build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. error 28-Nov-2024 18:22:55 2024/11/28 18:22:53:937 WARNING Starting without install4j classes build 28-Nov-2024 18:22:55 Please consult deprecation warnings for more details. build 28-Nov-2024 18:22:55 build 28-Nov-2024 18:22:55 BUILD SUCCESSFUL in 2m 23s build 28-Nov-2024 18:22:55 21 actionable tasks: 21 executed error 28-Nov-2024 18:22:55 2024/11/28 18:22:54:485 WARNING Starting without install4j classes simple 28-Nov-2024 18:22:55 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 28-Nov-2024 18:22:55 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 28-Nov-2024 18:22:55 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job #3 (JB-GDL46-JOB1-3)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL46-JOB1-3-ScriptBuildTask-3818133451752858650.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_dependency_parent_0=JB-GDB648-4\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_revision_number=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL46-JOB1-3\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL46-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL46-JOB1\nbamboo_shortPlanName=bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498225_previous_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_46498225_git_username=\nbamboo_buildNumber=3\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-GDL46-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_name=Jalview Git\nbamboo_shortPlanKey=GDL46\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_buildTimeStamp=2024-11-28T18:15:10.761Z\nbamboo_repository_previous_revision_number=f1f306f9af0fb1643345831b8880aebb526a5f61\nbamboo_repository_46498225_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildResultKey=JB-GDL46-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4492_gradle_build_not_excluding_classes - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\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-GDL46 -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_repository_46498225_revision_number=4aa30fa9dd69fe01111355dda8b970a6ad9fca4c\nbamboo_planRepository_branch=bug/JAL-4492_gradle_build_not_excluding_classes\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=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\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-46302049\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-GDL46-JOB1\nbamboo_planKey=JB-GDL46\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4492_gradle_build_not_excluding_classes\nbamboo_repository_46498225_git_branch=bug/JAL-4492_gradle_build_not_excluding_classes\n simple 28-Nov-2024 18:22:55 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 28-Nov-2024 18:22:55 Running post build plugin 'NCover Results Collector' simple 28-Nov-2024 18:22:55 Running post build plugin 'Artifact Copier' simple 28-Nov-2024 18:22:55 Publishing an artifact: getdown simple 28-Nov-2024 18:22:55 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 100.0 ms simple 28-Nov-2024 18:22:55 Running post build plugin 'Artifactory Release Management Staging' simple 28-Nov-2024 18:22:55 Running post build plugin 'Artifactory Build Info Copier' simple 28-Nov-2024 18:22:55 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 28-Nov-2024 18:22:55 Running post build plugin 'npm Cache Cleanup' simple 28-Nov-2024 18:22:55 Running post build plugin 'Clover Results Collector' simple 28-Nov-2024 18:22:55 Running post build plugin 'Docker Container Cleanup' simple 28-Nov-2024 18:22:55 Finalising the build... simple 28-Nov-2024 18:22:55 Stopping timer. simple 28-Nov-2024 18:22:55 Build JB-GDL46-JOB1-3 completed. simple 28-Nov-2024 18:22:55 Running on server: post build plugin 'NCover Results Collector' simple 28-Nov-2024 18:22:55 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 28-Nov-2024 18:22:55 Running on server: post build plugin 'Clover Delta Calculator' simple 28-Nov-2024 18:22:55 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 28-Nov-2024 18:22:55 All post build plugins have finished simple 28-Nov-2024 18:22:55 Generating build results summary... simple 28-Nov-2024 18:22:55 Saving build results to disk... simple 28-Nov-2024 18:22:55 Logging substituted variables... simple 28-Nov-2024 18:22:55 Indexing build results... simple 28-Nov-2024 18:22:55 Finished building JB-GDL46-JOB1-3.