simple	19-Nov-2025 15:19:49	Build Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job #1 (JB-GDI439-JOB1-1) started building on agent Default Agent
simple	19-Nov-2025 15:19:49	
simple	19-Nov-2025 15:19:49	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1
simple	19-Nov-2025 15:19:49	Executing build Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job #1 (JB-GDI439-JOB1-1)
simple	19-Nov-2025 15:19:49	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	19-Nov-2025 15:19:49	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1
simple	19-Nov-2025 15:19:49	Updating source code to revision: b0fd08a15bfaff92e5d6c81412f82b5902ac284e
simple	19-Nov-2025 15:19:50	Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	19-Nov-2025 15:19:50	Checking out revision b0fd08a15bfaff92e5d6c81412f82b5902ac284e.
simple	19-Nov-2025 15:19:50	Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/.git'.
simple	19-Nov-2025 15:19:50	Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1'...
simple	19-Nov-2025 15:19:50	done.
simple	19-Nov-2025 15:19:58	Switched to a new branch 'development/Release_2_11_5_Branch'
simple	19-Nov-2025 15:19:58	Branch development/Release_2_11_5_Branch set up to track remote branch development/Release_2_11_5_Branch from origin.
simple	19-Nov-2025 15:19:58	Updated source code to revision: b0fd08a15bfaff92e5d6c81412f82b5902ac284e
simple	19-Nov-2025 15:19:58	Finished task 'Checkout Default Repository' with result: Success
simple	19-Nov-2025 15:19:58	Running pre-build action: VCS Version Collector
simple	19-Nov-2025 15:19:58	Running pre-build action: Artifactory Release Staging
command	19-Nov-2025 15:19:58	Substituting variable: ${bamboo.planKey} with JB-GDI439
simple	19-Nov-2025 15:19:58	Starting task 'Jalview DEVELOP distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	19-Nov-2025 15:19:58	Bamboo Artifactory Plugin version: 2.6.2
command	19-Nov-2025 15:19:58	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job #1 (JB-GDI439-JOB1-1)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDI439 clean shadowJar installers\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1\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-GDI439-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDI439-JOB1\nbamboo_repository_46498596_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_46498596_git_branch=development/Release_2_11_5_Branch\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-GDI439-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch\nbamboo_shortPlanKey=GDI439\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_buildTimeStamp=2025-11-19T15:10:38.943Z\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDI439-JOB1-1\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nSHLVL=1\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498596_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nbamboo_dependenciesDisabled=false\nbamboo_repository_46498596_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\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=development/Release_2_11_5_Branch\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=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\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-46302763\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/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-GDI439-JOB1\nbamboo_planKey=JB-GDI439\nbamboo_repository_46498596_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498596_branch_name=development/Release_2_11_5_Branch\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n
build	19-Nov-2025 15:20:00	
build	19-Nov-2025 15:20:00	> Configure project :
build	19-Nov-2025 15:20:00	Using properties from file './utils/channels/develop/channel_gradle.properties'
build	19-Nov-2025 15:20:00	JALVIEW_VERSION is set to '2.11.5.1'
build	19-Nov-2025 15:20:00	HEADLESS BUILD
build	19-Nov-2025 15:20:00	J2S ENABLED
build	19-Nov-2025 15:20:00	Using a DEVELOP profile.
build	19-Nov-2025 15:20:00	eclipseDir exists
build	19-Nov-2025 15:20:01	
build	19-Nov-2025 15:20:01	> Task :clean
build	19-Nov-2025 15:20:01	> Task :cleanPackageDir UP-TO-DATE
build	19-Nov-2025 15:20:01	> Task :cleanInstallersDataFiles
build	19-Nov-2025 15:20:03	
build	19-Nov-2025 15:20:03	> Task :checkPython
build	19-Nov-2025 15:20:03	Using python 3.6.8 from /usr (python3)
build	19-Nov-2025 15:20:03	Using pip 21.3.1 from /usr/local/lib/python3.6/site-packages/pip (python 3.6)
build	19-Nov-2025 15:20:03	Using venv (in '.gradle/python')
build	19-Nov-2025 15:20:03	[python] python3 -m venv .gradle/python
build	19-Nov-2025 15:20:06	Using python 3.6.8 from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/.gradle/python (.gradle/python/bin/python)
build	19-Nov-2025 15:20:07	Using pip 9.0.3 from /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/.gradle/python/lib64/python3.6/site-packages (python 3.6)
build	19-Nov-2025 15:20:09	
build	19-Nov-2025 15:20:09	> Task :pipInstall
build	19-Nov-2025 15:20:09	[python] .gradle/python/bin/python -m pip install ds_store==1.3.0
build	19-Nov-2025 15:20:09		 Collecting ds_store==1.3.0
build	19-Nov-2025 15:20:09		   Cache entry deserialization failed, entry ignored
build	19-Nov-2025 15:20:09		   Cache entry deserialization failed, entry ignored
build	19-Nov-2025 15:20:09		   Downloading https://files.pythonhosted.org/packages/38/a1/cab1b1cf3387eec963a18706854facdc5b699f782985a0001579e5dd6cda/ds_store-1.3.0.tar.gz
build	19-Nov-2025 15:20:09		 Collecting mac_alias>=2.0.1 (from ds_store==1.3.0)
build	19-Nov-2025 15:20:09		   Cache entry deserialization failed, entry ignored
build	19-Nov-2025 15:20:09		   Cache entry deserialization failed, entry ignored
build	19-Nov-2025 15:20:09		   Downloading https://files.pythonhosted.org/packages/54/cf/d4379fc5a6c7835ef92ff8ca49e8dc1c5c51b3c72333a394118887c87a6d/mac_alias-2.2.0.tar.gz
build	19-Nov-2025 15:20:09		 Installing collected packages: mac-alias, ds-store
build	19-Nov-2025 15:20:09		   Running setup.py install for mac-alias: started
build	19-Nov-2025 15:20:09		     Running setup.py install for mac-alias: finished with status 'done'
build	19-Nov-2025 15:20:09		   Running setup.py install for ds-store: started
build	19-Nov-2025 15:20:10		     Running setup.py install for ds-store: finished with status 'done'
build	19-Nov-2025 15:20:10		 Successfully installed ds-store-1.3.0 mac-alias-2.2.0
build	19-Nov-2025 15:20:10		 You are using pip version 9.0.3, however version 25.3 is available.
build	19-Nov-2025 15:20:10		 You should consider upgrading via the 'pip install --upgrade pip' command.
build	19-Nov-2025 15:20:10	[python] .gradle/python/bin/python -m pip list --format=columns
build	19-Nov-2025 15:20:11		 Package    Version
build	19-Nov-2025 15:20:11		 ---------- -------
build	19-Nov-2025 15:20:11		 ds-store   1.3.0  
build	19-Nov-2025 15:20:11		 mac-alias  2.2.0  
build	19-Nov-2025 15:20:11		 pip        9.0.3  
build	19-Nov-2025 15:20:11		 setuptools 39.2.0 
build	19-Nov-2025 15:20:11		 You are using pip version 9.0.3, however version 25.3 is available.
build	19-Nov-2025 15:20:11		 You should consider upgrading via the 'pip install --upgrade pip' command.
build	19-Nov-2025 15:20:11	
build	19-Nov-2025 15:20:11	> Task :copyHelp
build	19-Nov-2025 15:20:14	> Task :buildIndices
build	19-Nov-2025 15:20:14	> Task :copyResources
build	19-Nov-2025 15:20:14	> Task :copyChannelResources
build	19-Nov-2025 15:20:14	
build	19-Nov-2025 15:20:14	> Task :createBuildProperties
build	19-Nov-2025 15:20:14	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:20:14	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:14	
build	19-Nov-2025 15:20:14	> Task :buildResources
build	19-Nov-2025 15:20:14	> Task :copyDocs
build	19-Nov-2025 15:20:15	
build	19-Nov-2025 15:20:15	> Task :convertMdFiles
build	19-Nov-2025 15:20:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	19-Nov-2025 15:20:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	19-Nov-2025 15:20:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	19-Nov-2025 15:20:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/resources/doc_build/doc/building.html
build	19-Nov-2025 15:20:15	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	19-Nov-2025 15:20:15	
build	19-Nov-2025 15:20:15	> Task :releasesTemplates
build	19-Nov-2025 15:20:15	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:20:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:15	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:15	Stripping rc/test/etc for 2_11_5_1-d20251119
build	19-Nov-2025 15:20:15	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	19-Nov-2025 15:20:15	
build	19-Nov-2025 15:20:15	> Task :prepare
build	19-Nov-2025 15:20:18	
build	19-Nov-2025 15:20:18	> Task :compileJava
build	19-Nov-2025 15:20:18	Setting target compatibility to 11
build	19-Nov-2025 15:20:26	
build	19-Nov-2025 15:20:26	> Task :processResources
build	19-Nov-2025 15:20:26	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:26	
build	19-Nov-2025 15:20:26	> Task :classes
error	19-Nov-2025 15:20:26	Note: Some input files use or override a deprecated API.
error	19-Nov-2025 15:20:26	Note: Recompile with -Xlint:deprecation for details.
error	19-Nov-2025 15:20:26	Note: Some input files use unchecked or unsafe operations.
error	19-Nov-2025 15:20:26	Note: Recompile with -Xlint:unchecked for details.
build	19-Nov-2025 15:20:29	
build	19-Nov-2025 15:20:29	> Task :compileLinkCheck
build	19-Nov-2025 15:20:29	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:20:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:29	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-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	19-Nov-2025 15:20:31	
build	19-Nov-2025 15:20:31	> Task :linkCheck
build	19-Nov-2025 15:20:31	Checking help file links
build	19-Nov-2025 15:22:38	
build	19-Nov-2025 15:22:38	Results:
build	19-Nov-2025 15:22:38	161 distinct help targets
build	19-Nov-2025 15:22:38	161 help mappings
build	19-Nov-2025 15:22:38	0 invalid targets
build	19-Nov-2025 15:22:38	31 unused targets
build	19-Nov-2025 15:22:38	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	19-Nov-2025 15:22:38	    overviewprefs: html/features/preferences.html#overview
build	19-Nov-2025 15:22:38	    cdnafeatures: html/features/codingfeatures.html
build	19-Nov-2025 15:22:38	    startupprefs: html/features/preferences.html#startup
build	19-Nov-2025 15:22:38	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	19-Nov-2025 15:22:38	    io.modellerpir: html/io/modellerpir.html
build	19-Nov-2025 15:22:38	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	19-Nov-2025 15:22:38	    pdbmcviewer: html/features/pdbviewer.html
build	19-Nov-2025 15:22:38	    groovy.colours: html/features/groovy.html#groovyColours
build	19-Nov-2025 15:22:38	    seqmappings: html/features/seqmappings.html
build	19-Nov-2025 15:22:38	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	19-Nov-2025 15:22:38	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	19-Nov-2025 15:22:38	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	19-Nov-2025 15:22:38	    search: html/features/search.html
build	19-Nov-2025 15:22:38	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	19-Nov-2025 15:22:38	    alformats: html/io/fileformats.html
build	19-Nov-2025 15:22:38	    strucprefs: html/features/preferences.html#structure
build	19-Nov-2025 15:22:38	    siftsmapping: html/features/siftsmapping.html
build	19-Nov-2025 15:22:38	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	19-Nov-2025 15:22:38	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	19-Nov-2025 15:22:38	    newkeys: html/features/newkeystrokes.html
build	19-Nov-2025 15:22:38	    importvcf.attribs: html/features/importvcf.html#attribs
build	19-Nov-2025 15:22:38	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	19-Nov-2025 15:22:38	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	19-Nov-2025 15:22:38	    jalarchive: html/features/jalarchive.html
build	19-Nov-2025 15:22:38	    newsreader: html/webServices/newsreader.html
build	19-Nov-2025 15:22:38	    jalviewcltool: html/features/commandline.html#script
build	19-Nov-2025 15:22:38	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	19-Nov-2025 15:22:38	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	19-Nov-2025 15:22:38	    paematrixformat: html/io/paematrixformat.html
build	19-Nov-2025 15:22:38	    overview: html/features/overview.html
build	19-Nov-2025 15:22:38	0 invalid map urls
build	19-Nov-2025 15:22:38	0 invalid image attributes
build	19-Nov-2025 15:22:38	520 internal href links (120 with anchors)
build	19-Nov-2025 15:22:38	0 invalid internal href links
build	19-Nov-2025 15:22:38	0 invalid internal anchor links
build	19-Nov-2025 15:22:38	112 external href links
build	19-Nov-2025 15:22:38	External links not verified as internet not available
build	19-Nov-2025 15:22:38	*** Success ***
build	19-Nov-2025 15:22:39	
build	19-Nov-2025 15:22:39	> Task :jar
build	19-Nov-2025 15:22:39	> Task :syncJars
build	19-Nov-2025 15:22:39	> Task :makeDist
build	19-Nov-2025 15:22:47	> Task :shadowJar
build	19-Nov-2025 15:22:47	
build	19-Nov-2025 15:22:47	> Task :copyInstall4jTemplate
build	19-Nov-2025 15:22:47	Execution optimizations have been disabled for task ':copyInstall4jTemplate' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/file_associations_auto-install4j10.xml'. Reason: Task ':copyInstall4jTemplate' 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	19-Nov-2025 15:22:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/install4j11_template.install4j'. Reason: Task ':copyInstall4jTemplate' 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	19-Nov-2025 15:22:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/jalview-install4j-conf.install4j'. Reason: Task ':compileLinkCheck' uses this output of task ':copyInstall4jTemplate' 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	19-Nov-2025 15:22:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/jalview-install4j-conf.install4j'. Reason: Task ':linkCheck' uses this output of task ':copyInstall4jTemplate' 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	19-Nov-2025 15:22:47	Using '.VolumeIcon.icns' file 'utils/channels/develop/images/jalview_develop-VolumeIcon.icns'
build	19-Nov-2025 15:22:47	
build	19-Nov-2025 15:22:47	> Task :getdownImagesCopy
build	19-Nov-2025 15:22:47	Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:47	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images'. 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	19-Nov-2025 15:22:48	
build	19-Nov-2025 15:22:48	> Task :getdownImagesProcess
build	19-Nov-2025 15:22:48	> Task :getdownImages
build	19-Nov-2025 15:22:49	> Task :getdownWebsiteBuild
build	19-Nov-2025 15:22:50	
build	19-Nov-2025 15:22:50	> Task :getdownDigest
build	19-Nov-2025 15:22:50	Generating digest file './build/website/docroot/getdown/develop/11/digest.txt'...
build	19-Nov-2025 15:22:50	Generating digest file './build/website/docroot/getdown/develop/11/digest2.txt'...
build	19-Nov-2025 15:22:50	
build	19-Nov-2025 15:22:50	> Task :getdown
build	19-Nov-2025 15:22:50	LIKELY RSYNC COMMAND:
build	19-Nov-2025 15:22:50	mkdir -p '/Volumes/jalview/docroot/getdown/develop/11/'
build	19-Nov-2025 15:22:50	rsync -avh --delete './build/website/docroot/getdown/develop/11/' '/Volumes/jalview/docroot/getdown/develop/11/'
error	19-Nov-2025 15:22:50	2025/11/19 15:22:49:020 WARNING Starting without install4j classes
error	19-Nov-2025 15:22:50	2025/11/19 15:22:49:692 WARNING Starting without install4j classes
build	19-Nov-2025 15:22:50	
build	19-Nov-2025 15:22:50	> Task :install4jCustomiseDS_StoreAarch64
build	19-Nov-2025 15:22:50	Execution optimizations have been disabled for task ':install4jCustomiseDS_StoreAarch64' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images/jalview_develop_dmg_DS_Store'. Reason: Task ':install4jCustomiseDS_StoreAarch64' 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	19-Nov-2025 15:22:50	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images/jalview_develop_dmg_DS_Store.json'. Reason: Task ':install4jCustomiseDS_StoreAarch64' 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	19-Nov-2025 15:22:50	Running command 'utils/macos_dmg/jalview_customise_dsstore.py --input "utils/channels/develop/images/jalview_develop_dmg_DS_Store" --output "build/macos_dmg/jalview_develop_dmg_DS_Store-aarch64" --volumename "Install Jalview Develop 2.11.5.1-d20251119 (Apple Silicon)" --backgroundfile "background.png" --dmg "Jalview_Develop-2.11.5.1-d20251119-macos-aarch64-java_11.dmg" --appname "Jalview Develop.app" --config "utils/channels/develop/images/jalview_develop_dmg_DS_Store.json"'
build	19-Nov-2025 15:22:50	[python] .gradle/python/bin/python utils/macos_dmg/jalview_customise_dsstore.py --input utils/channels/develop/images/jalview_develop_dmg_DS_Store --output build/macos_dmg/jalview_develop_dmg_DS_Store-aarch64 --volumename Install Jalview Develop 2.11.5.1-d20251119 (Apple Silicon) --backgroundfile background.png --dmg Jalview_Develop-2.11.5.1-d20251119-macos-aarch64-java_11.dmg --appname Jalview Develop.app --config utils/channels/develop/images/jalview_develop_dmg_DS_Store.json
build	19-Nov-2025 15:22:50		 Setting bwsp['ShowStatusBar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['SidebarWidthTenElevenOrLater'] to '160.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['ShowToolbar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['ShowTabView'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['ContainerShowSidebar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['WindowBounds'] to '{{800, 600}, {490, 370}}' from config
build	19-Nov-2025 15:22:50		 Setting bwsp['ShowSidebar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting bwsp['ShowPathbar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['backgroundImageAlias']
build	19-Nov-2025 15:22:50		 Setting icvp['backgroundColorRed'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['backgroundColorBlue'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['backgroundColorGreen'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['gridSpacing'] to '43.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['gridOffsetX'] to '0.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['gridOffsetY'] to '0.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['showItemInfo'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['viewOptionsVersion'] to '1' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['arrangeBy'] to 'none' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['textSize'] to '12.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['labelOnBottom'] to 'True' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['backgroundType'] to '2' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['showIconPreview'] to 'True' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icvp['iconSize'] to '76.0' from input DS_Store
build	19-Nov-2025 15:22:50		 Setting icon location for filename 'Install Jalview.app' to ( 244, 60 )
build	19-Nov-2025 15:22:50		 Setting icon location for filename 'Jalview Develop.app' to ( 244, 200 )
build	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jCustomiseDS_StoreX64
build	19-Nov-2025 15:22:51	Execution optimizations have been disabled for task ':install4jCustomiseDS_StoreX64' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images/jalview_develop_dmg_DS_Store'. Reason: Task ':install4jCustomiseDS_StoreX64' 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	19-Nov-2025 15:22:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images/jalview_develop_dmg_DS_Store.json'. Reason: Task ':install4jCustomiseDS_StoreX64' 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	19-Nov-2025 15:22:51	Running command 'utils/macos_dmg/jalview_customise_dsstore.py --input utils/channels/develop/images/jalview_develop_dmg_DS_Store --output build/macos_dmg/jalview_develop_dmg_DS_Store-x64 --volumename Install Jalview Develop 2.11.5.1-d20251119 (Intel) --backgroundfile background.png --dmg Jalview_Develop-2.11.5.1-d20251119-macos-x64-java_11.dmg --appname Jalview Develop.app --config utils/channels/develop/images/jalview_develop_dmg_DS_Store.json'
build	19-Nov-2025 15:22:51	[python] .gradle/python/bin/python utils/macos_dmg/jalview_customise_dsstore.py --input utils/channels/develop/images/jalview_develop_dmg_DS_Store --output build/macos_dmg/jalview_develop_dmg_DS_Store-x64 --volumename Install Jalview Develop 2.11.5.1-d20251119 (Intel) --backgroundfile background.png --dmg Jalview_Develop-2.11.5.1-d20251119-macos-x64-java_11.dmg --appname Jalview Develop.app --config utils/channels/develop/images/jalview_develop_dmg_DS_Store.json
build	19-Nov-2025 15:22:51		 Setting bwsp['ShowStatusBar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['SidebarWidthTenElevenOrLater'] to '160.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['ShowToolbar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['ShowTabView'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['ContainerShowSidebar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['WindowBounds'] to '{{800, 600}, {490, 370}}' from config
build	19-Nov-2025 15:22:51		 Setting bwsp['ShowSidebar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting bwsp['ShowPathbar'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['backgroundImageAlias']
build	19-Nov-2025 15:22:51		 Setting icvp['backgroundColorRed'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['backgroundColorBlue'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['backgroundColorGreen'] to '1.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['gridSpacing'] to '43.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['gridOffsetX'] to '0.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['gridOffsetY'] to '0.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['showItemInfo'] to 'False' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['viewOptionsVersion'] to '1' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['arrangeBy'] to 'none' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['textSize'] to '12.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['labelOnBottom'] to 'True' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['backgroundType'] to '2' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['showIconPreview'] to 'True' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icvp['iconSize'] to '76.0' from input DS_Store
build	19-Nov-2025 15:22:51		 Setting icon location for filename 'Install Jalview.app' to ( 244, 60 )
build	19-Nov-2025 15:22:51		 Setting icon location for filename 'Jalview Develop.app' to ( 244, 200 )
build	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jCustomiseDS_Store
build	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jDMGBackgroundImageCopy
build	19-Nov-2025 15:22:51	Execution optimizations have been disabled for task ':install4jDMGBackgroundImageCopy' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/channels/develop/images/jalview_develop_dmg_background-72dpi.png'. Reason: Task ':install4jDMGBackgroundImageCopy' 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	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jDMGBackgroundImageProcess
build	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jDMGVmoptionsFile
build	19-Nov-2025 15:22:51	Execution optimizations have been disabled for task ':install4jDMGVmoptionsFile' to ensure correctness due to the following reasons:
build	19-Nov-2025 15:22:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j'. Reason: Task ':install4jDMGVmoptionsFile' 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	19-Nov-2025 15:22:51	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/default.vmoptions'. Reason: Task ':install4jDMGVmoptionsFile' 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	19-Nov-2025 15:22:51	
build	19-Nov-2025 15:22:51	> Task :install4jDMGProcesses
build	19-Nov-2025 15:22:53	
build	19-Nov-2025 15:22:53	> Task :installerFiles
build	19-Nov-2025 15:22:53	Using projectFile task ':installerFiles' property 'projectFile'
build	19-Nov-2025 15:22:53	Downloading install4j 11.0.5
build	19-Nov-2025 15:23:03	install4j version 11.0.5 (build 11153), built on 2025-08-04
build	19-Nov-2025 15:23:03	Registered to 
build	19-Nov-2025 15:23:03	
build	19-Nov-2025 15:23:03	Loading config file /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/jalview-install4j-conf.install4j
build	19-Nov-2025 15:23:04	[WARNING] The JDK with name "JDK 11.0" has not been configured in this install4j installation (config file /srv/bamboo/home/bamboo/.config/install4j/v11/config.xml).
build	19-Nov-2025 15:23:04	          As a fallback, a suitable JDK will be downloaded with the settings from the "General Settings->JRE Bundles" step.
build	19-Nov-2025 15:23:04	          
build	19-Nov-2025 15:23:04	          To set up the named JDK, add the line
build	19-Nov-2025 15:23:04	          
build	19-Nov-2025 15:23:04	          -DJDK_11.0=<path to JDK home>
build	19-Nov-2025 15:23:04	          
build	19-Nov-2025 15:23:04	          in the file /srv/bamboo/home/bamboo/.gradle/install4j/dist/11.0.5/bin/install4j.vmoptions
build	19-Nov-2025 15:23:04	Finding JDK release 11/latest [linux-amd64]
build	19-Nov-2025 15:23:05	Downloading OpenJDK11U-jdk_x64_linux_hotspot_11.0.29_7.tar.gz
build	19-Nov-2025 15:23:15	Processing downloaded JDK archive
build	19-Nov-2025 15:23:17	Extracting JDK
build	19-Nov-2025 15:23:20	Creating media file 'Windows x64 EXE Installer':
build	19-Nov-2025 15:23:21	  Collecting files:
build	19-Nov-2025 15:23:21	  Compiling launchers:
build	19-Nov-2025 15:23:21	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:21	      Generating VM options file jalviewg.vmoptions.
build	19-Nov-2025 15:23:21	  Creating media file: 
build	19-Nov-2025 15:23:21	    Using custom installer icon: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/../../utils/channels/develop/images/jalview_develop_logo.ico
build	19-Nov-2025 15:23:24	    Zipping custom code & resources JAR file
build	19-Nov-2025 15:23:24	    Identifying components
build	19-Nov-2025 15:23:24	    Adding JRE (jre_11_windows_x64.tar.gz)
build	19-Nov-2025 15:23:24	    Shrinking runtime
build	19-Nov-2025 15:23:25	  
build	19-Nov-2025 15:23:25	Creating media file 'macOS (Intel) Disk Image':
build	19-Nov-2025 15:23:25	  Collecting files:
build	19-Nov-2025 15:23:25	  Compiling launchers:
build	19-Nov-2025 15:23:25	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:25	      Generating VM options file vmoptions.txt.
build	19-Nov-2025 15:23:25	  Creating media file: 
build	19-Nov-2025 15:23:26	      Extracting archive /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/../../utils/macos_dmg/Install Jalview/Install Jalview_app.tgz with DMG top-level files
build	19-Nov-2025 15:23:26	      Shrinking runtime
build	19-Nov-2025 15:23:27	  
build	19-Nov-2025 15:23:27	Creating media file 'macOS (Apple Silicon) Disk Image':
build	19-Nov-2025 15:23:27	  Collecting files:
build	19-Nov-2025 15:23:27	  Compiling launchers:
build	19-Nov-2025 15:23:27	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:27	      Generating VM options file vmoptions.txt.
build	19-Nov-2025 15:23:27	  Creating media file: 
build	19-Nov-2025 15:23:27	      Extracting archive /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/utils/install4j/../../utils/macos_dmg/Install Jalview/Install Jalview_app.tgz with DMG top-level files
build	19-Nov-2025 15:23:27	      Shrinking runtime
build	19-Nov-2025 15:23:28	  
build	19-Nov-2025 15:23:28	Creating media file 'Linux x64 Shell Installer':
build	19-Nov-2025 15:23:30	  Collecting files:
build	19-Nov-2025 15:23:30	  Compiling launchers:
build	19-Nov-2025 15:23:30	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:30	      Generating launcher script file
build	19-Nov-2025 15:23:30	      Generating VM options file .i4j_external_735/jalviewg.vmoptions.
build	19-Nov-2025 15:23:30	  Creating media file: 
build	19-Nov-2025 15:23:30	    Generating launcher script file
build	19-Nov-2025 15:23:31	    Zipping custom code & resources JAR file
build	19-Nov-2025 15:23:31	    Identifying components
build	19-Nov-2025 15:23:31	    Adding JRE (jre_11_linux_x64.tar.gz)
build	19-Nov-2025 15:23:31	    Shrinking runtime
build	19-Nov-2025 15:23:31	  
build	19-Nov-2025 15:23:31	Creating media file 'Linux aarch64 Shell Installer':
build	19-Nov-2025 15:23:33	  Collecting files:
build	19-Nov-2025 15:23:33	  Compiling launchers:
build	19-Nov-2025 15:23:33	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:33	      Generating launcher script file
build	19-Nov-2025 15:23:33	      Generating VM options file .i4j_external_735/jalviewg.vmoptions.
build	19-Nov-2025 15:23:33	  Creating media file: 
build	19-Nov-2025 15:23:33	    Generating launcher script file
build	19-Nov-2025 15:23:33	    Zipping custom code & resources JAR file
build	19-Nov-2025 15:23:33	    Identifying components
build	19-Nov-2025 15:23:33	    Adding JRE (jre_11_linux_aarch64.tar.gz)
build	19-Nov-2025 15:23:33	    Shrinking runtime
build	19-Nov-2025 15:23:35	  
build	19-Nov-2025 15:23:35	Creating media file 'Unix .tar.gz Archive':
build	19-Nov-2025 15:23:35	  Collecting files:
build	19-Nov-2025 15:23:35	  Compiling launchers:
build	19-Nov-2025 15:23:35	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:35	      Generating launcher script file
build	19-Nov-2025 15:23:35	      Generating VM options file .i4j_external_735/jalviewg.vmoptions.
build	19-Nov-2025 15:23:35	  Creating media file: 
build	19-Nov-2025 15:23:35	      Shrinking runtime
build	19-Nov-2025 15:23:35	  
build	19-Nov-2025 15:23:35	Creating media file 'Unix Shell Installer':
build	19-Nov-2025 15:23:35	  Collecting files:
build	19-Nov-2025 15:23:35	  Compiling launchers:
build	19-Nov-2025 15:23:35	    Compiling launcher 'Jalview User Launcher':
build	19-Nov-2025 15:23:35	      Generating launcher script file
build	19-Nov-2025 15:23:35	      Generating VM options file .i4j_external_735/jalviewg.vmoptions.
build	19-Nov-2025 15:23:35	  Creating media file: 
build	19-Nov-2025 15:23:35	    Generating launcher script file
build	19-Nov-2025 15:23:35	    Zipping custom code & resources JAR file
build	19-Nov-2025 15:23:35	    Identifying components
build	19-Nov-2025 15:23:35	    Shrinking runtime
build	19-Nov-2025 15:23:37	  
build	19-Nov-2025 15:23:37	Compressing 7 media files with 4 threads:
build	19-Nov-2025 15:24:13	
build	19-Nov-2025 15:24:13	Compressed media file 'Unix Shell Installer':
build	19-Nov-2025 15:24:13	  Compressing files
build	19-Nov-2025 15:24:13	  Applying LZMA compression
build	19-Nov-2025 15:24:13	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:13	  The name of the media file is jalview_develop-2_11_5_1-d20251119-unix-java_11.sh.
build	19-Nov-2025 15:24:13	  The size of the media file is 52.1 MB
build	19-Nov-2025 15:24:16	
build	19-Nov-2025 15:24:16	Compressed media file 'Linux x64 Shell Installer':
build	19-Nov-2025 15:24:16	  Compressing files
build	19-Nov-2025 15:24:16	  Applying LZMA compression
build	19-Nov-2025 15:24:16	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:16	  The name of the media file is jalview_develop-2_11_5_1-d20251119-linux-x64-java_11.sh.
build	19-Nov-2025 15:24:16	  The size of the media file is 93.0 MB
build	19-Nov-2025 15:24:16	
build	19-Nov-2025 15:24:16	Compressed media file 'Linux aarch64 Shell Installer':
build	19-Nov-2025 15:24:16	  Compressing files
build	19-Nov-2025 15:24:16	  Applying LZMA compression
build	19-Nov-2025 15:24:16	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:16	  The name of the media file is jalview_develop-2_11_5_1-d20251119-linux-aarch64-java_11.sh.
build	19-Nov-2025 15:24:16	  The size of the media file is 91.5 MB
build	19-Nov-2025 15:24:16	
build	19-Nov-2025 15:24:16	Compressed media file 'Windows x64 EXE Installer':
build	19-Nov-2025 15:24:16	  Compressing files
build	19-Nov-2025 15:24:16	  Applying LZMA compression
build	19-Nov-2025 15:24:16	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:16	  The name of the media file is Jalview_Develop-2_11_5_1-d20251119-windows-x64-java_11.exe.
build	19-Nov-2025 15:24:16	  The size of the media file is 95.5 MB
build	19-Nov-2025 15:24:18	
build	19-Nov-2025 15:24:18	Compressed media file 'Unix .tar.gz Archive':
build	19-Nov-2025 15:24:18	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:18	  The name of the media file is jalview_develop-2_11_5_1-d20251119-unix-java_11.tar.gz.
build	19-Nov-2025 15:24:18	  The size of the media file is 53.2 MB
build	19-Nov-2025 15:24:31	
build	19-Nov-2025 15:24:31	Compressed media file 'macOS (Intel) Disk Image':
build	19-Nov-2025 15:24:31	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:31	  The name of the media file is Jalview_Develop-2_11_5_1-d20251119-macos-x64-java_11.dmg.
build	19-Nov-2025 15:24:31	  The size of the media file is 96.6 MB
build	19-Nov-2025 15:24:33	
build	19-Nov-2025 15:24:33	Compressed media file 'macOS (Apple Silicon) Disk Image':
build	19-Nov-2025 15:24:33	  Moving media files to media directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/build/install4j/11
build	19-Nov-2025 15:24:33	  The name of the media file is Jalview_Develop-2_11_5_1-d20251119-macos-aarch64-java_11.dmg.
build	19-Nov-2025 15:24:33	  The size of the media file is 95.4 MB
build	19-Nov-2025 15:24:33	Writing md5sums.
build	19-Nov-2025 15:24:33	Writing sha256sums.
build	19-Nov-2025 15:24:33	Writing updates.xml.
build	19-Nov-2025 15:24:33	Please upload updates.xml to https://www.jalview.org/install4j/updates.xml
build	19-Nov-2025 15:24:33	and upload all generated media files to the same directory.
build	19-Nov-2025 15:24:33	
build	19-Nov-2025 15:24:33	Build completed in 90.1 seconds at 2025-11-19 15:24:33 with 1 warning.
build	19-Nov-2025 15:24:33	Run the build in verbose mode to get instructions on how to suppress selected warnings.
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	> Task :installers
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	Execution optimizations have been disabled for 10 invalid unit(s) of work during this build to ensure correctness.
build	19-Nov-2025 15:24:35	Please consult deprecation warnings for more details.
build	19-Nov-2025 15:24:35	
build	19-Nov-2025 15:24:35	BUILD SUCCESSFUL in 4m 36s
build	19-Nov-2025 15:24:35	32 actionable tasks: 31 executed, 1 up-to-date
simple	19-Nov-2025 15:24:36	Finished task 'Jalview DEVELOP distribution for Java 11' with result: Success
simple	19-Nov-2025 15:24:36	Starting task 'Create tar of DEVELOP channel installers' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	19-Nov-2025 15:24:36	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job #1 (JB-GDI439-JOB1-1)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDI439-JOB1-1-ScriptBuildTask-3156143052934788813.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=development/Release_2_11_5_Branch\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch\nbamboo_repository_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDI439-JOB1\nbamboo_repository_46498596_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_shortPlanName=development-Release_2_11_5_Branch\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_repository_46498596_git_branch=development/Release_2_11_5_Branch\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-GDI439-JOB1-1\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch\nbamboo_shortPlanKey=GDI439\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_buildTimeStamp=2025-11-19T15:10:38.943Z\nbamboo_repository_git_branch=development/Release_2_11_5_Branch\nbamboo_buildResultKey=JB-GDI439-JOB1-1\nbamboo_repository_branch_name=development/Release_2_11_5_Branch\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_repository_46498596_name=Jalview Gitlab\nbamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDI439 clean shadowJar installers\nbamboo_dependenciesDisabled=false\nbamboo_repository_46498596_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=development/Release_2_11_5_Branch\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=development/Release_2_11_5_Branch\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=development/Release_2_11_5_Branch\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-46302763\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_ManualBuildTriggerReason_userName=jprocter\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/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-GDI439-JOB1\nbamboo_planKey=JB-GDI439\nbamboo_repository_46498596_git_username=\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498596_branch_name=development/Release_2_11_5_Branch\nbamboo_planRepository_1_branchName=development/Release_2_11_5_Branch\n
build	19-Nov-2025 15:24:36	installers/
build	19-Nov-2025 15:24:36	installers/tmp/
build	19-Nov-2025 15:24:36	installers/tmp/default.vmoptions.AARCH64
build	19-Nov-2025 15:24:36	installers/tmp/default.vmoptions.X64
build	19-Nov-2025 15:24:36	installers/11/
build	19-Nov-2025 15:24:36	installers/11/Jalview_Develop-2_11_5_1-d20251119-windows-x64-java_11.exe
build	19-Nov-2025 15:24:40	installers/11/jalview_develop-2_11_5_1-d20251119-unix-java_11.sh
build	19-Nov-2025 15:24:41	installers/11/sha256sums
build	19-Nov-2025 15:24:41	installers/11/md5sums
build	19-Nov-2025 15:24:41	installers/11/jalview_develop-2_11_5_1-d20251119-unix-java_11.tar.gz
build	19-Nov-2025 15:24:43	installers/11/output.txt
build	19-Nov-2025 15:24:43	installers/11/jalview_develop-2_11_5_1-d20251119-linux-x64-java_11.sh
build	19-Nov-2025 15:24:46	installers/11/Jalview_Develop-2_11_5_1-d20251119-macos-aarch64-java_11.dmg
build	19-Nov-2025 15:24:50	installers/11/jalview_develop-2_11_5_1-d20251119-linux-aarch64-java_11.sh
build	19-Nov-2025 15:24:53	installers/11/Jalview_Develop-2_11_5_1-d20251119-macos-x64-java_11.dmg
build	19-Nov-2025 15:24:56	installers/11/updates.xml
simple	19-Nov-2025 15:24:56	Finished task 'Create tar of DEVELOP channel installers' with result: Success
simple	19-Nov-2025 15:24:56	Running post build plugin 'NCover Results Collector'
simple	19-Nov-2025 15:24:56	Running post build plugin 'Artifact Copier'
simple	19-Nov-2025 15:24:56	Publishing an artifact: develop_installers_tar
simple	19-Nov-2025 15:24:58	Finished publishing of artifact Shared artifact: [develop_installers_tar], pattern: [develop_installers.tgz] anchored at: [build] in 1.829 s
simple	19-Nov-2025 15:24:58	Running post build plugin 'Artifactory Release Management Staging'
simple	19-Nov-2025 15:24:58	Running post build plugin 'Artifactory Build Info Copier'
simple	19-Nov-2025 15:24:58	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	19-Nov-2025 15:24:58	Running post build plugin 'npm Cache Cleanup'
simple	19-Nov-2025 15:24:58	Running post build plugin 'Clover Results Collector'
simple	19-Nov-2025 15:24:58	Running post build plugin 'Docker Container Cleanup'
simple	19-Nov-2025 15:24:58	Finalising the build...
simple	19-Nov-2025 15:24:58	Stopping timer.
simple	19-Nov-2025 15:24:58	Build JB-GDI439-JOB1-1 completed.
simple	19-Nov-2025 15:24:58	Running on server: post build plugin 'NCover Results Collector'
simple	19-Nov-2025 15:24:58	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	19-Nov-2025 15:24:58	Running on server: post build plugin 'Clover Delta Calculator'
simple	19-Nov-2025 15:24:58	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	19-Nov-2025 15:24:58	All post build plugins have finished
simple	19-Nov-2025 15:24:58	Generating build results summary...
simple	19-Nov-2025 15:24:58	Saving build results to disk...
simple	19-Nov-2025 15:24:58	Logging substituted variables...
simple	19-Nov-2025 15:24:58	Indexing build results...
simple	19-Nov-2025 15:24:58	Finished building JB-GDI439-JOB1-1.