simple 05-Nov-2025 13:26:49 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job #1 (JB-GDL96-JOB1-1) started building on agent Default Agent simple 05-Nov-2025 13:26:49 simple 05-Nov-2025 13:26:49 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1 simple 05-Nov-2025 13:26:49 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job #1 (JB-GDL96-JOB1-1) simple 05-Nov-2025 13:26:49 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 05-Nov-2025 13:26:49 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1 simple 05-Nov-2025 13:26:49 Updating source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553 simple 05-Nov-2025 13:26:49 Fetching 'refs/heads/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 05-Nov-2025 13:26:50 Checking out revision 0d10b35174aa38a4a48c5965e683dabe47dcd553. simple 05-Nov-2025 13:26:50 Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/.git'. simple 05-Nov-2025 13:26:50 Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1'... simple 05-Nov-2025 13:26:50 done. simple 05-Nov-2025 13:26:57 Switched to a new branch 'bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection' simple 05-Nov-2025 13:26:57 Branch bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection set up to track remote branch bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection from origin. simple 05-Nov-2025 13:26:57 Updated source code to revision: 0d10b35174aa38a4a48c5965e683dabe47dcd553 simple 05-Nov-2025 13:26:57 Finished task 'Checkout Default Repository' with result: Success simple 05-Nov-2025 13:26:57 Running pre-build action: VCS Version Collector simple 05-Nov-2025 13:26:57 Running pre-build action: Artifactory Release Staging command 05-Nov-2025 13:26:57 Substituting variable: ${bamboo.planKey} with JB-GDL96 simple 05-Nov-2025 13:26:57 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 05-Nov-2025 13:26:57 Bamboo Artifactory Plugin version: 2.6.2 command 05-Nov-2025 13:26:57 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job #1 (JB-GDL96-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL96 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_dependency_parent_0=JB-GDB714-3\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-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL96-JOB1-1\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_repository_46498509_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL96-JOB1\nbamboo_shortPlanName=bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498509_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=1\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-GDL96-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498509_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_shortPlanKey=GDL96\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_buildTimeStamp=2025-11-05T13:26:49.495Z\nbamboo_repository_46498509_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_repository_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildResultKey=JB-GDL96-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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-46302589\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_repository_46498509_name=Jalview Gitlab\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498509_git_username=\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-GDL96-JOB1\nbamboo_planKey=JB-GDL96\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 05-Nov-2025 13:27:00 build 05-Nov-2025 13:27:00 > Configure project : build 05-Nov-2025 13:27:00 Using properties from file './utils/channels/default/channel_gradle.properties' build 05-Nov-2025 13:27:00 JALVIEW_VERSION is set to '2.11.5.1' build 05-Nov-2025 13:27:00 HEADLESS BUILD build 05-Nov-2025 13:27:00 J2S ENABLED build 05-Nov-2025 13:27:00 Using a BUILD profile. build 05-Nov-2025 13:27:00 eclipseDir exists build 05-Nov-2025 13:27:00 build 05-Nov-2025 13:27:00 > Task :clean build 05-Nov-2025 13:27:00 > Task :cleanPackageDir UP-TO-DATE build 05-Nov-2025 13:27:00 > Task :getdownImagesCopy build 05-Nov-2025 13:27:00 > Task :getdownImagesProcess build 05-Nov-2025 13:27:00 > Task :getdownImages build 05-Nov-2025 13:27:00 > Task :copyHelp build 05-Nov-2025 13:27:03 > Task :buildIndices build 05-Nov-2025 13:27:03 > Task :copyResources build 05-Nov-2025 13:27:03 > Task :copyChannelResources build 05-Nov-2025 13:27:04 build 05-Nov-2025 13:27:04 > Task :createBuildProperties build 05-Nov-2025 13:27:04 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 05-Nov-2025 13:27:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:04 build 05-Nov-2025 13:27:04 > Task :buildResources build 05-Nov-2025 13:27:04 > Task :copyDocs build 05-Nov-2025 13:27:04 build 05-Nov-2025 13:27:04 > Task :convertMdFiles build 05-Nov-2025 13:27:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 05-Nov-2025 13:27:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/build/resources/doc_build/doc/releaseprocess.html build 05-Nov-2025 13:27:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 05-Nov-2025 13:27:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/build/resources/doc_build/doc/building.html build 05-Nov-2025 13:27:04 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/build/resources/doc_build/doc/jalview-projects.html build 05-Nov-2025 13:27:04 build 05-Nov-2025 13:27:04 > Task :releasesTemplates build 05-Nov-2025 13:27:04 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 05-Nov-2025 13:27:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:04 Stripping rc/test/etc for 2_11_5_1 build 05-Nov-2025 13:27:04 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 05-Nov-2025 13:27:04 build 05-Nov-2025 13:27:04 > Task :prepare build 05-Nov-2025 13:27:07 build 05-Nov-2025 13:27:07 > Task :compileJava build 05-Nov-2025 13:27:07 Setting target compatibility to 11 build 05-Nov-2025 13:27:16 build 05-Nov-2025 13:27:16 > Task :processResources build 05-Nov-2025 13:27:16 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:16 build 05-Nov-2025 13:27:16 > Task :classes error 05-Nov-2025 13:27:16 Note: Some input files use or override a deprecated API. error 05-Nov-2025 13:27:16 Note: Recompile with -Xlint:deprecation for details. error 05-Nov-2025 13:27:16 Note: Some input files use unchecked or unsafe operations. error 05-Nov-2025 13:27:16 Note: Recompile with -Xlint:unchecked for details. build 05-Nov-2025 13:27:18 build 05-Nov-2025 13:27:18 > Task :compileLinkCheck build 05-Nov-2025 13:27:18 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 05-Nov-2025 13:27:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:18 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-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 05-Nov-2025 13:27:21 build 05-Nov-2025 13:27:21 > Task :linkCheck build 05-Nov-2025 13:27:21 Checking help file links build 05-Nov-2025 13:29:28 build 05-Nov-2025 13:29:28 Results: build 05-Nov-2025 13:29:28 161 distinct help targets build 05-Nov-2025 13:29:28 161 help mappings build 05-Nov-2025 13:29:28 0 invalid targets build 05-Nov-2025 13:29:28 31 unused targets build 05-Nov-2025 13:29:28 uniprotfetcher: html/features/uniprotsequencefetcher.html build 05-Nov-2025 13:29:28 overviewprefs: html/features/preferences.html#overview build 05-Nov-2025 13:29:28 cdnafeatures: html/features/codingfeatures.html build 05-Nov-2025 13:29:28 startupprefs: html/features/preferences.html#startup build 05-Nov-2025 13:29:28 ensemblfetch: html/features/ensemblsequencefetcher.html build 05-Nov-2025 13:29:28 io.modellerpir: html/io/modellerpir.html build 05-Nov-2025 13:29:28 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 05-Nov-2025 13:29:28 pdbmcviewer: html/features/pdbviewer.html build 05-Nov-2025 13:29:28 groovy.colours: html/features/groovy.html#groovyColours build 05-Nov-2025 13:29:28 seqmappings: html/features/seqmappings.html build 05-Nov-2025 13:29:28 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 05-Nov-2025 13:29:28 splitframe.mirrorfonts: html/features/splitView.html#mirror build 05-Nov-2025 13:29:28 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 05-Nov-2025 13:29:28 search: html/features/search.html build 05-Nov-2025 13:29:28 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 05-Nov-2025 13:29:28 alformats: html/io/fileformats.html build 05-Nov-2025 13:29:28 strucprefs: html/features/preferences.html#structure build 05-Nov-2025 13:29:28 siftsmapping: html/features/siftsmapping.html build 05-Nov-2025 13:29:28 chimera.annotxfer: html/features/chimera.html#annotxfer build 05-Nov-2025 13:29:28 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 05-Nov-2025 13:29:28 newkeys: html/features/newkeystrokes.html build 05-Nov-2025 13:29:28 importvcf.attribs: html/features/importvcf.html#attribs build 05-Nov-2025 13:29:28 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 05-Nov-2025 13:29:28 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 05-Nov-2025 13:29:28 jalarchive: html/features/jalarchive.html build 05-Nov-2025 13:29:28 newsreader: html/webServices/newsreader.html build 05-Nov-2025 13:29:28 jalviewcltool: html/features/commandline.html#script build 05-Nov-2025 13:29:28 popMenuAddref: html/menus/popupMenu.html#addrefannot build 05-Nov-2025 13:29:28 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 05-Nov-2025 13:29:28 paematrixformat: html/io/paematrixformat.html build 05-Nov-2025 13:29:28 overview: html/features/overview.html build 05-Nov-2025 13:29:28 0 invalid map urls build 05-Nov-2025 13:29:28 0 invalid image attributes build 05-Nov-2025 13:29:28 520 internal href links (120 with anchors) build 05-Nov-2025 13:29:28 0 invalid internal href links build 05-Nov-2025 13:29:28 0 invalid internal anchor links build 05-Nov-2025 13:29:28 112 external href links build 05-Nov-2025 13:29:28 External links not verified as internet not available build 05-Nov-2025 13:29:28 *** Success *** build 05-Nov-2025 13:29:29 build 05-Nov-2025 13:29:29 > Task :jar build 05-Nov-2025 13:29:29 > Task :syncJars build 05-Nov-2025 13:29:29 > Task :makeDist build 05-Nov-2025 13:29:29 > Task :getdownWebsiteBuild error 05-Nov-2025 13:29:31 2025/11/05 13:29:29:885 WARNING Starting without install4j classes error 05-Nov-2025 13:29:31 2025/11/05 13:29:30:486 WARNING Starting without install4j classes build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 > Task :getdownDigest build 05-Nov-2025 13:29:31 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 05-Nov-2025 13:29:31 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 > Task :getdown build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 05-Nov-2025 13:29:31 Please consult deprecation warnings for more details. build 05-Nov-2025 13:29:31 build 05-Nov-2025 13:29:31 BUILD SUCCESSFUL in 2m 33s build 05-Nov-2025 13:29:31 21 actionable tasks: 20 executed, 1 up-to-date simple 05-Nov-2025 13:29:31 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 05-Nov-2025 13:29:31 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 05-Nov-2025 13:29:31 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job #1 (JB-GDL96-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL96-JOB1-1-ScriptBuildTask-5015132754340404999.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_dependency_parent_0=JB-GDB714-3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL96-JOB1-1\nbamboo_repository_46498509_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL96-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL96-JOB1\nbamboo_shortPlanName=bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_repository_46498509_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=1\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-GDL96-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498509_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_shortPlanKey=GDL96\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_buildTimeStamp=2025-11-05T13:26:49.495Z\nbamboo_repository_46498509_revision_number=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_repository_git_branch=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildResultKey=JB-GDL96-JOB1-1\nbamboo_repository_branch_name=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=0d10b35174aa38a4a48c5965e683dabe47dcd553\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\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-GDL96 -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=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\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-46302589\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_repository_46498509_name=Jalview Gitlab\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498509_git_username=\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-GDL96-JOB1\nbamboo_planKey=JB-GDL96\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection\n simple 05-Nov-2025 13:29:31 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 05-Nov-2025 13:29:31 Running post build plugin 'NCover Results Collector' simple 05-Nov-2025 13:29:31 Running post build plugin 'Artifact Copier' simple 05-Nov-2025 13:29:31 Publishing an artifact: getdown simple 05-Nov-2025 13:29:32 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 146.4 ms simple 05-Nov-2025 13:29:32 Running post build plugin 'Artifactory Release Management Staging' simple 05-Nov-2025 13:29:32 Running post build plugin 'Artifactory Build Info Copier' simple 05-Nov-2025 13:29:32 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 05-Nov-2025 13:29:32 Running post build plugin 'npm Cache Cleanup' simple 05-Nov-2025 13:29:32 Running post build plugin 'Clover Results Collector' simple 05-Nov-2025 13:29:32 Running post build plugin 'Docker Container Cleanup' simple 05-Nov-2025 13:29:32 Finalising the build... simple 05-Nov-2025 13:29:32 Stopping timer. simple 05-Nov-2025 13:29:32 Build JB-GDL96-JOB1-1 completed. simple 05-Nov-2025 13:29:32 Running on server: post build plugin 'NCover Results Collector' simple 05-Nov-2025 13:29:32 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 05-Nov-2025 13:29:32 Running on server: post build plugin 'Clover Delta Calculator' simple 05-Nov-2025 13:29:32 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 05-Nov-2025 13:29:32 All post build plugins have finished simple 05-Nov-2025 13:29:32 Generating build results summary... simple 05-Nov-2025 13:29:32 Saving build results to disk... simple 05-Nov-2025 13:29:32 Logging substituted variables... simple 05-Nov-2025 13:29:32 Indexing build results... simple 05-Nov-2025 13:29:32 Finished building JB-GDL96-JOB1-1.