Create installers for Jalview Develop edition
Build: #1 was successful
Job: Default Job was successful
Build log
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| 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 |
| 19-Nov-2025 15:19:49 | |
| 19-Nov-2025 15:19:49 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 |
| 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) |
| 19-Nov-2025 15:19:49 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 19-Nov-2025 15:19:49 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 |
| 19-Nov-2025 15:19:49 | Updating source code to revision: b0fd08a15bfaff92e5d6c81412f82b5902ac284e |
| 19-Nov-2025 15:19:50 | Fetching 'refs/heads/development/Release_2_11_5_Branch' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 19-Nov-2025 15:19:50 | Checking out revision b0fd08a15bfaff92e5d6c81412f82b5902ac284e. |
| 19-Nov-2025 15:19:50 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1/.git'. |
| 19-Nov-2025 15:19:50 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1'... |
| 19-Nov-2025 15:19:50 | done. |
| 19-Nov-2025 15:19:58 | Switched to a new branch 'development/Release_2_11_5_Branch' |
| 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. |
| 19-Nov-2025 15:19:58 | Updated source code to revision: b0fd08a15bfaff92e5d6c81412f82b5902ac284e |
| 19-Nov-2025 15:19:58 | Finished task 'Checkout Default Repository' with result: Success |
| 19-Nov-2025 15:19:58 | Running pre-build action: VCS Version Collector |
| 19-Nov-2025 15:19:58 | Running pre-build action: Artifactory Release Staging |
| 19-Nov-2025 15:19:58 | Substituting variable: ${bamboo.planKey} with JB-GDI439 |
| 19-Nov-2025 15:19:58 | Starting task 'Jalview DEVELOP distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 19-Nov-2025 15:19:58 | Bamboo Artifactory Plugin version: 2.6.2 |
| 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)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=DEVELOP -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDI439 clean shadowJar installers ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=development/Release_2_11_5_Branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch bamboo_repository_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDI439-JOB1 bamboo_repository_46498596_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortPlanName=development-Release_2_11_5_Branch bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_repository_46498596_git_branch=development/Release_2_11_5_Branch bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch bamboo_shortPlanKey=GDI439 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_buildTimeStamp=2025-11-19T15:10:38.943Z bamboo_repository_git_branch=development/Release_2_11_5_Branch bamboo_buildResultKey=JB-GDI439-JOB1-1 bamboo_repository_branch_name=development/Release_2_11_5_Branch bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_repository_46498596_name=Jalview Gitlab JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_dependenciesDisabled=false bamboo_repository_46498596_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=development/Release_2_11_5_Branch bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=development/Release_2_11_5_Branch _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46302763 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 bamboo_planKey=JB-GDI439 bamboo_repository_46498596_git_username= bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498596_branch_name=development/Release_2_11_5_Branch HOME=/home/bamboo bamboo_planRepository_1_branchName=development/Release_2_11_5_Branch PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 19-Nov-2025 15:20:00 | |
| 19-Nov-2025 15:20:00 | > Configure project : |
| 19-Nov-2025 15:20:00 | Using properties from file './utils/channels/develop/channel_gradle.properties' |
| 19-Nov-2025 15:20:00 | JALVIEW_VERSION is set to '2.11.5.1' |
| 19-Nov-2025 15:20:00 | HEADLESS BUILD |
| 19-Nov-2025 15:20:00 | J2S ENABLED |
| 19-Nov-2025 15:20:00 | Using a DEVELOP profile. |
| 19-Nov-2025 15:20:00 | eclipseDir exists |
| 19-Nov-2025 15:20:01 | |
| 19-Nov-2025 15:20:01 | > Task :clean |
| 19-Nov-2025 15:20:01 | > Task :cleanPackageDir UP-TO-DATE |
| 19-Nov-2025 15:20:01 | > Task :cleanInstallersDataFiles |
| 19-Nov-2025 15:20:03 | |
| 19-Nov-2025 15:20:03 | > Task :checkPython |
| 19-Nov-2025 15:20:03 | Using python 3.6.8 from /usr (python3) |
| 19-Nov-2025 15:20:03 | Using pip 21.3.1 from /usr/local/lib/python3.6/site-packages/pip (python 3.6) |
| 19-Nov-2025 15:20:03 | Using venv (in '.gradle/python') |
| 19-Nov-2025 15:20:03 | [python] python3 -m venv .gradle/python |
| 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) |
| 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) |
| 19-Nov-2025 15:20:09 | |
| 19-Nov-2025 15:20:09 | > Task :pipInstall |
| 19-Nov-2025 15:20:09 | [python] .gradle/python/bin/python -m pip install ds_store==1.3.0 |
| 19-Nov-2025 15:20:09 | Collecting ds_store==1.3.0 |
| 19-Nov-2025 15:20:09 | Cache entry deserialization failed, entry ignored |
| 19-Nov-2025 15:20:09 | Cache entry deserialization failed, entry ignored |
| 19-Nov-2025 15:20:09 | Downloading https://files.pythonhosted.org/packages/38/a1/cab1b1cf3387eec963a18706854facdc5b699f782985a0001579e5dd6cda/ds_store-1.3.0.tar.gz |
| 19-Nov-2025 15:20:09 | Collecting mac_alias>=2.0.1 (from ds_store==1.3.0) |
| 19-Nov-2025 15:20:09 | Cache entry deserialization failed, entry ignored |
| 19-Nov-2025 15:20:09 | Cache entry deserialization failed, entry ignored |
| 19-Nov-2025 15:20:09 | Downloading https://files.pythonhosted.org/packages/54/cf/d4379fc5a6c7835ef92ff8ca49e8dc1c5c51b3c72333a394118887c87a6d/mac_alias-2.2.0.tar.gz |
| 19-Nov-2025 15:20:09 | Installing collected packages: mac-alias, ds-store |
| 19-Nov-2025 15:20:09 | Running setup.py install for mac-alias: started |
| 19-Nov-2025 15:20:09 | Running setup.py install for mac-alias: finished with status 'done' |
| 19-Nov-2025 15:20:09 | Running setup.py install for ds-store: started |
| 19-Nov-2025 15:20:10 | Running setup.py install for ds-store: finished with status 'done' |
| 19-Nov-2025 15:20:10 | Successfully installed ds-store-1.3.0 mac-alias-2.2.0 |
| 19-Nov-2025 15:20:10 | You are using pip version 9.0.3, however version 25.3 is available. |
| 19-Nov-2025 15:20:10 | You should consider upgrading via the 'pip install --upgrade pip' command. |
| 19-Nov-2025 15:20:10 | [python] .gradle/python/bin/python -m pip list --format=columns |
| 19-Nov-2025 15:20:11 | Package Version |
| 19-Nov-2025 15:20:11 | ---------- ------- |
| 19-Nov-2025 15:20:11 | ds-store 1.3.0 |
| 19-Nov-2025 15:20:11 | mac-alias 2.2.0 |
| 19-Nov-2025 15:20:11 | pip 9.0.3 |
| 19-Nov-2025 15:20:11 | setuptools 39.2.0 |
| 19-Nov-2025 15:20:11 | You are using pip version 9.0.3, however version 25.3 is available. |
| 19-Nov-2025 15:20:11 | You should consider upgrading via the 'pip install --upgrade pip' command. |
| 19-Nov-2025 15:20:11 | |
| 19-Nov-2025 15:20:11 | > Task :copyHelp |
| 19-Nov-2025 15:20:14 | > Task :buildIndices |
| 19-Nov-2025 15:20:14 | > Task :copyResources |
| 19-Nov-2025 15:20:14 | > Task :copyChannelResources |
| 19-Nov-2025 15:20:14 | |
| 19-Nov-2025 15:20:14 | > Task :createBuildProperties |
| 19-Nov-2025 15:20:14 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 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. |
| 19-Nov-2025 15:20:14 | |
| 19-Nov-2025 15:20:14 | > Task :buildResources |
| 19-Nov-2025 15:20:14 | > Task :copyDocs |
| 19-Nov-2025 15:20:15 | |
| 19-Nov-2025 15:20:15 | > Task :convertMdFiles |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 19-Nov-2025 15:20:15 | |
| 19-Nov-2025 15:20:15 | > Task :releasesTemplates |
| 19-Nov-2025 15:20:15 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 19-Nov-2025 15:20:15 | Stripping rc/test/etc for 2_11_5_1-d20251119 |
| 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 |
| 19-Nov-2025 15:20:15 | |
| 19-Nov-2025 15:20:15 | > Task :prepare |
| 19-Nov-2025 15:20:18 | |
| 19-Nov-2025 15:20:18 | > Task :compileJava |
| 19-Nov-2025 15:20:18 | Setting target compatibility to 11 |
| 19-Nov-2025 15:20:26 | |
| 19-Nov-2025 15:20:26 | > Task :processResources |
| 19-Nov-2025 15:20:26 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 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. |
| 19-Nov-2025 15:20:26 | |
| 19-Nov-2025 15:20:26 | > Task :classes |
| 19-Nov-2025 15:20:26 | Note: Some input files use or override a deprecated API. |
| 19-Nov-2025 15:20:26 | Note: Recompile with -Xlint:deprecation for details. |
| 19-Nov-2025 15:20:26 | Note: Some input files use unchecked or unsafe operations. |
| 19-Nov-2025 15:20:26 | Note: Recompile with -Xlint:unchecked for details. |
| 19-Nov-2025 15:20:29 | |
| 19-Nov-2025 15:20:29 | > Task :compileLinkCheck |
| 19-Nov-2025 15:20:29 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 19-Nov-2025 15:20:31 | |
| 19-Nov-2025 15:20:31 | > Task :linkCheck |
| 19-Nov-2025 15:20:31 | Checking help file links |
| 19-Nov-2025 15:22:38 | |
| 19-Nov-2025 15:22:38 | Results: |
| 19-Nov-2025 15:22:38 | 161 distinct help targets |
| 19-Nov-2025 15:22:38 | 161 help mappings |
| 19-Nov-2025 15:22:38 | 0 invalid targets |
| 19-Nov-2025 15:22:38 | 31 unused targets |
| 19-Nov-2025 15:22:38 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 19-Nov-2025 15:22:38 | overviewprefs: html/features/preferences.html#overview |
| 19-Nov-2025 15:22:38 | cdnafeatures: html/features/codingfeatures.html |
| 19-Nov-2025 15:22:38 | startupprefs: html/features/preferences.html#startup |
| 19-Nov-2025 15:22:38 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 19-Nov-2025 15:22:38 | io.modellerpir: html/io/modellerpir.html |
| 19-Nov-2025 15:22:38 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 19-Nov-2025 15:22:38 | pdbmcviewer: html/features/pdbviewer.html |
| 19-Nov-2025 15:22:38 | groovy.colours: html/features/groovy.html#groovyColours |
| 19-Nov-2025 15:22:38 | seqmappings: html/features/seqmappings.html |
| 19-Nov-2025 15:22:38 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 19-Nov-2025 15:22:38 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 19-Nov-2025 15:22:38 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 19-Nov-2025 15:22:38 | search: html/features/search.html |
| 19-Nov-2025 15:22:38 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 19-Nov-2025 15:22:38 | alformats: html/io/fileformats.html |
| 19-Nov-2025 15:22:38 | strucprefs: html/features/preferences.html#structure |
| 19-Nov-2025 15:22:38 | siftsmapping: html/features/siftsmapping.html |
| 19-Nov-2025 15:22:38 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 19-Nov-2025 15:22:38 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 19-Nov-2025 15:22:38 | newkeys: html/features/newkeystrokes.html |
| 19-Nov-2025 15:22:38 | importvcf.attribs: html/features/importvcf.html#attribs |
| 19-Nov-2025 15:22:38 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 19-Nov-2025 15:22:38 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 19-Nov-2025 15:22:38 | jalarchive: html/features/jalarchive.html |
| 19-Nov-2025 15:22:38 | newsreader: html/webServices/newsreader.html |
| 19-Nov-2025 15:22:38 | jalviewcltool: html/features/commandline.html#script |
| 19-Nov-2025 15:22:38 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 19-Nov-2025 15:22:38 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 19-Nov-2025 15:22:38 | paematrixformat: html/io/paematrixformat.html |
| 19-Nov-2025 15:22:38 | overview: html/features/overview.html |
| 19-Nov-2025 15:22:38 | 0 invalid map urls |
| 19-Nov-2025 15:22:38 | 0 invalid image attributes |
| 19-Nov-2025 15:22:38 | 520 internal href links (120 with anchors) |
| 19-Nov-2025 15:22:38 | 0 invalid internal href links |
| 19-Nov-2025 15:22:38 | 0 invalid internal anchor links |
| 19-Nov-2025 15:22:38 | 112 external href links |
| 19-Nov-2025 15:22:38 | External links not verified as internet not available |
| 19-Nov-2025 15:22:38 | *** Success *** |
| 19-Nov-2025 15:22:39 | |
| 19-Nov-2025 15:22:39 | > Task :jar |
| 19-Nov-2025 15:22:39 | > Task :syncJars |
| 19-Nov-2025 15:22:39 | > Task :makeDist |
| 19-Nov-2025 15:22:47 | > Task :shadowJar |
| 19-Nov-2025 15:22:47 | |
| 19-Nov-2025 15:22:47 | > Task :copyInstall4jTemplate |
| 19-Nov-2025 15:22:47 | Execution optimizations have been disabled for task ':copyInstall4jTemplate' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 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. |
| 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. |
| 19-Nov-2025 15:22:47 | Using '.VolumeIcon.icns' file 'utils/channels/develop/images/jalview_develop-VolumeIcon.icns' |
| 19-Nov-2025 15:22:47 | |
| 19-Nov-2025 15:22:47 | > Task :getdownImagesCopy |
| 19-Nov-2025 15:22:47 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 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. |
| 19-Nov-2025 15:22:48 | |
| 19-Nov-2025 15:22:48 | > Task :getdownImagesProcess |
| 19-Nov-2025 15:22:48 | > Task :getdownImages |
| 19-Nov-2025 15:22:49 | > Task :getdownWebsiteBuild |
| 19-Nov-2025 15:22:50 | |
| 19-Nov-2025 15:22:50 | > Task :getdownDigest |
| 19-Nov-2025 15:22:50 | Generating digest file './build/website/docroot/getdown/develop/11/digest.txt'... |
| 19-Nov-2025 15:22:50 | Generating digest file './build/website/docroot/getdown/develop/11/digest2.txt'... |
| 19-Nov-2025 15:22:50 | |
| 19-Nov-2025 15:22:50 | > Task :getdown |
| 19-Nov-2025 15:22:50 | LIKELY RSYNC COMMAND: |
| 19-Nov-2025 15:22:50 | mkdir -p '/Volumes/jalview/docroot/getdown/develop/11/' |
| 19-Nov-2025 15:22:50 | rsync -avh --delete './build/website/docroot/getdown/develop/11/' '/Volumes/jalview/docroot/getdown/develop/11/' |
| 19-Nov-2025 15:22:50 | 2025/11/19 15:22:49:020 WARNING Starting without install4j classes |
| 19-Nov-2025 15:22:50 | 2025/11/19 15:22:49:692 WARNING Starting without install4j classes |
| 19-Nov-2025 15:22:50 | |
| 19-Nov-2025 15:22:50 | > Task :install4jCustomiseDS_StoreAarch64 |
| 19-Nov-2025 15:22:50 | Execution optimizations have been disabled for task ':install4jCustomiseDS_StoreAarch64' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 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"' |
| 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 |
| 19-Nov-2025 15:22:50 | Setting bwsp['ShowStatusBar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['SidebarWidthTenElevenOrLater'] to '160.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['ShowToolbar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['ShowTabView'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['ContainerShowSidebar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['WindowBounds'] to '{{800, 600}, {490, 370}}' from config |
| 19-Nov-2025 15:22:50 | Setting bwsp['ShowSidebar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting bwsp['ShowPathbar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['backgroundImageAlias'] |
| 19-Nov-2025 15:22:50 | Setting icvp['backgroundColorRed'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['backgroundColorBlue'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['backgroundColorGreen'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['gridSpacing'] to '43.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['gridOffsetX'] to '0.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['gridOffsetY'] to '0.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['showItemInfo'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['viewOptionsVersion'] to '1' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['arrangeBy'] to 'none' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['textSize'] to '12.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['labelOnBottom'] to 'True' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['backgroundType'] to '2' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['showIconPreview'] to 'True' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icvp['iconSize'] to '76.0' from input DS_Store |
| 19-Nov-2025 15:22:50 | Setting icon location for filename 'Install Jalview.app' to ( 244, 60 ) |
| 19-Nov-2025 15:22:50 | Setting icon location for filename 'Jalview Develop.app' to ( 244, 200 ) |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jCustomiseDS_StoreX64 |
| 19-Nov-2025 15:22:51 | Execution optimizations have been disabled for task ':install4jCustomiseDS_StoreX64' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 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' |
| 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 |
| 19-Nov-2025 15:22:51 | Setting bwsp['ShowStatusBar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['SidebarWidthTenElevenOrLater'] to '160.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['ShowToolbar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['ShowTabView'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['ContainerShowSidebar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['WindowBounds'] to '{{800, 600}, {490, 370}}' from config |
| 19-Nov-2025 15:22:51 | Setting bwsp['ShowSidebar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting bwsp['ShowPathbar'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['backgroundImageAlias'] |
| 19-Nov-2025 15:22:51 | Setting icvp['backgroundColorRed'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['backgroundColorBlue'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['backgroundColorGreen'] to '1.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['gridSpacing'] to '43.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['gridOffsetX'] to '0.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['gridOffsetY'] to '0.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['showItemInfo'] to 'False' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['viewOptionsVersion'] to '1' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['arrangeBy'] to 'none' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['textSize'] to '12.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['labelOnBottom'] to 'True' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['backgroundType'] to '2' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['showIconPreview'] to 'True' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icvp['iconSize'] to '76.0' from input DS_Store |
| 19-Nov-2025 15:22:51 | Setting icon location for filename 'Install Jalview.app' to ( 244, 60 ) |
| 19-Nov-2025 15:22:51 | Setting icon location for filename 'Jalview Develop.app' to ( 244, 200 ) |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jCustomiseDS_Store |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jDMGBackgroundImageCopy |
| 19-Nov-2025 15:22:51 | Execution optimizations have been disabled for task ':install4jDMGBackgroundImageCopy' to ensure correctness due to the following reasons: |
| 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. |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jDMGBackgroundImageProcess |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jDMGVmoptionsFile |
| 19-Nov-2025 15:22:51 | Execution optimizations have been disabled for task ':install4jDMGVmoptionsFile' to ensure correctness due to the following reasons: |
| 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. |
| 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. |
| 19-Nov-2025 15:22:51 | |
| 19-Nov-2025 15:22:51 | > Task :install4jDMGProcesses |
| 19-Nov-2025 15:22:53 | |
| 19-Nov-2025 15:22:53 | > Task :installerFiles |
| 19-Nov-2025 15:22:53 | Using projectFile task ':installerFiles' property 'projectFile' |
| 19-Nov-2025 15:22:53 | Downloading install4j 11.0.5 |
| 19-Nov-2025 15:23:03 | install4j version 11.0.5 (build 11153), built on 2025-08-04 |
| 19-Nov-2025 15:23:03 | Registered to |
| 19-Nov-2025 15:23:03 | |
| 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 |
| 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). |
| 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. |
| 19-Nov-2025 15:23:04 | |
| 19-Nov-2025 15:23:04 | To set up the named JDK, add the line |
| 19-Nov-2025 15:23:04 | |
| 19-Nov-2025 15:23:04 | -DJDK_11.0=<path to JDK home> |
| 19-Nov-2025 15:23:04 | |
| 19-Nov-2025 15:23:04 | in the file /srv/bamboo/home/bamboo/.gradle/install4j/dist/11.0.5/bin/install4j.vmoptions |
| 19-Nov-2025 15:23:04 | Finding JDK release 11/latest [linux-amd64] |
| 19-Nov-2025 15:23:05 | Downloading OpenJDK11U-jdk_x64_linux_hotspot_11.0.29_7.tar.gz |
| 19-Nov-2025 15:23:15 | Processing downloaded JDK archive |
| 19-Nov-2025 15:23:17 | Extracting JDK |
| 19-Nov-2025 15:23:20 | Creating media file 'Windows x64 EXE Installer': |
| 19-Nov-2025 15:23:21 | Collecting files: |
| 19-Nov-2025 15:23:21 | Compiling launchers: |
| 19-Nov-2025 15:23:21 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:21 | Generating VM options file jalviewg.vmoptions. |
| 19-Nov-2025 15:23:21 | Creating media file: |
| 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 |
| 19-Nov-2025 15:23:24 | Zipping custom code & resources JAR file |
| 19-Nov-2025 15:23:24 | Identifying components |
| 19-Nov-2025 15:23:24 | Adding JRE (jre_11_windows_x64.tar.gz) |
| 19-Nov-2025 15:23:24 | Shrinking runtime |
| 19-Nov-2025 15:23:25 | |
| 19-Nov-2025 15:23:25 | Creating media file 'macOS (Intel) Disk Image': |
| 19-Nov-2025 15:23:25 | Collecting files: |
| 19-Nov-2025 15:23:25 | Compiling launchers: |
| 19-Nov-2025 15:23:25 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:25 | Generating VM options file vmoptions.txt. |
| 19-Nov-2025 15:23:25 | Creating media file: |
| 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 |
| 19-Nov-2025 15:23:26 | Shrinking runtime |
| 19-Nov-2025 15:23:27 | |
| 19-Nov-2025 15:23:27 | Creating media file 'macOS (Apple Silicon) Disk Image': |
| 19-Nov-2025 15:23:27 | Collecting files: |
| 19-Nov-2025 15:23:27 | Compiling launchers: |
| 19-Nov-2025 15:23:27 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:27 | Generating VM options file vmoptions.txt. |
| 19-Nov-2025 15:23:27 | Creating media file: |
| 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 |
| 19-Nov-2025 15:23:27 | Shrinking runtime |
| 19-Nov-2025 15:23:28 | |
| 19-Nov-2025 15:23:28 | Creating media file 'Linux x64 Shell Installer': |
| 19-Nov-2025 15:23:30 | Collecting files: |
| 19-Nov-2025 15:23:30 | Compiling launchers: |
| 19-Nov-2025 15:23:30 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:30 | Generating launcher script file |
| 19-Nov-2025 15:23:30 | Generating VM options file .i4j_external_735/jalviewg.vmoptions. |
| 19-Nov-2025 15:23:30 | Creating media file: |
| 19-Nov-2025 15:23:30 | Generating launcher script file |
| 19-Nov-2025 15:23:31 | Zipping custom code & resources JAR file |
| 19-Nov-2025 15:23:31 | Identifying components |
| 19-Nov-2025 15:23:31 | Adding JRE (jre_11_linux_x64.tar.gz) |
| 19-Nov-2025 15:23:31 | Shrinking runtime |
| 19-Nov-2025 15:23:31 | |
| 19-Nov-2025 15:23:31 | Creating media file 'Linux aarch64 Shell Installer': |
| 19-Nov-2025 15:23:33 | Collecting files: |
| 19-Nov-2025 15:23:33 | Compiling launchers: |
| 19-Nov-2025 15:23:33 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:33 | Generating launcher script file |
| 19-Nov-2025 15:23:33 | Generating VM options file .i4j_external_735/jalviewg.vmoptions. |
| 19-Nov-2025 15:23:33 | Creating media file: |
| 19-Nov-2025 15:23:33 | Generating launcher script file |
| 19-Nov-2025 15:23:33 | Zipping custom code & resources JAR file |
| 19-Nov-2025 15:23:33 | Identifying components |
| 19-Nov-2025 15:23:33 | Adding JRE (jre_11_linux_aarch64.tar.gz) |
| 19-Nov-2025 15:23:33 | Shrinking runtime |
| 19-Nov-2025 15:23:35 | |
| 19-Nov-2025 15:23:35 | Creating media file 'Unix .tar.gz Archive': |
| 19-Nov-2025 15:23:35 | Collecting files: |
| 19-Nov-2025 15:23:35 | Compiling launchers: |
| 19-Nov-2025 15:23:35 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:35 | Generating launcher script file |
| 19-Nov-2025 15:23:35 | Generating VM options file .i4j_external_735/jalviewg.vmoptions. |
| 19-Nov-2025 15:23:35 | Creating media file: |
| 19-Nov-2025 15:23:35 | Shrinking runtime |
| 19-Nov-2025 15:23:35 | |
| 19-Nov-2025 15:23:35 | Creating media file 'Unix Shell Installer': |
| 19-Nov-2025 15:23:35 | Collecting files: |
| 19-Nov-2025 15:23:35 | Compiling launchers: |
| 19-Nov-2025 15:23:35 | Compiling launcher 'Jalview User Launcher': |
| 19-Nov-2025 15:23:35 | Generating launcher script file |
| 19-Nov-2025 15:23:35 | Generating VM options file .i4j_external_735/jalviewg.vmoptions. |
| 19-Nov-2025 15:23:35 | Creating media file: |
| 19-Nov-2025 15:23:35 | Generating launcher script file |
| 19-Nov-2025 15:23:35 | Zipping custom code & resources JAR file |
| 19-Nov-2025 15:23:35 | Identifying components |
| 19-Nov-2025 15:23:35 | Shrinking runtime |
| 19-Nov-2025 15:23:37 | |
| 19-Nov-2025 15:23:37 | Compressing 7 media files with 4 threads: |
| 19-Nov-2025 15:24:13 | |
| 19-Nov-2025 15:24:13 | Compressed media file 'Unix Shell Installer': |
| 19-Nov-2025 15:24:13 | Compressing files |
| 19-Nov-2025 15:24:13 | Applying LZMA compression |
| 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 |
| 19-Nov-2025 15:24:13 | The name of the media file is jalview_develop-2_11_5_1-d20251119-unix-java_11.sh. |
| 19-Nov-2025 15:24:13 | The size of the media file is 52.1 MB |
| 19-Nov-2025 15:24:16 | |
| 19-Nov-2025 15:24:16 | Compressed media file 'Linux x64 Shell Installer': |
| 19-Nov-2025 15:24:16 | Compressing files |
| 19-Nov-2025 15:24:16 | Applying LZMA compression |
| 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 |
| 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. |
| 19-Nov-2025 15:24:16 | The size of the media file is 93.0 MB |
| 19-Nov-2025 15:24:16 | |
| 19-Nov-2025 15:24:16 | Compressed media file 'Linux aarch64 Shell Installer': |
| 19-Nov-2025 15:24:16 | Compressing files |
| 19-Nov-2025 15:24:16 | Applying LZMA compression |
| 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 |
| 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. |
| 19-Nov-2025 15:24:16 | The size of the media file is 91.5 MB |
| 19-Nov-2025 15:24:16 | |
| 19-Nov-2025 15:24:16 | Compressed media file 'Windows x64 EXE Installer': |
| 19-Nov-2025 15:24:16 | Compressing files |
| 19-Nov-2025 15:24:16 | Applying LZMA compression |
| 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 |
| 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. |
| 19-Nov-2025 15:24:16 | The size of the media file is 95.5 MB |
| 19-Nov-2025 15:24:18 | |
| 19-Nov-2025 15:24:18 | Compressed media file 'Unix .tar.gz Archive': |
| 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 |
| 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. |
| 19-Nov-2025 15:24:18 | The size of the media file is 53.2 MB |
| 19-Nov-2025 15:24:31 | |
| 19-Nov-2025 15:24:31 | Compressed media file 'macOS (Intel) Disk Image': |
| 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 |
| 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. |
| 19-Nov-2025 15:24:31 | The size of the media file is 96.6 MB |
| 19-Nov-2025 15:24:33 | |
| 19-Nov-2025 15:24:33 | Compressed media file 'macOS (Apple Silicon) Disk Image': |
| 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 |
| 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. |
| 19-Nov-2025 15:24:33 | The size of the media file is 95.4 MB |
| 19-Nov-2025 15:24:33 | Writing md5sums. |
| 19-Nov-2025 15:24:33 | Writing sha256sums. |
| 19-Nov-2025 15:24:33 | Writing updates.xml. |
| 19-Nov-2025 15:24:33 | Please upload updates.xml to https://www.jalview.org/install4j/updates.xml |
| 19-Nov-2025 15:24:33 | and upload all generated media files to the same directory. |
| 19-Nov-2025 15:24:33 | |
| 19-Nov-2025 15:24:33 | Build completed in 90.1 seconds at 2025-11-19 15:24:33 with 1 warning. |
| 19-Nov-2025 15:24:33 | Run the build in verbose mode to get instructions on how to suppress selected warnings. |
| 19-Nov-2025 15:24:35 | |
| 19-Nov-2025 15:24:35 | > Task :installers |
| 19-Nov-2025 15:24:35 | |
| 19-Nov-2025 15:24:35 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 19-Nov-2025 15:24:35 | |
| 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. |
| 19-Nov-2025 15:24:35 | |
| 19-Nov-2025 15:24:35 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 19-Nov-2025 15:24:35 | |
| 19-Nov-2025 15:24:35 | Execution optimizations have been disabled for 10 invalid unit(s) of work during this build to ensure correctness. |
| 19-Nov-2025 15:24:35 | Please consult deprecation warnings for more details. |
| 19-Nov-2025 15:24:35 | |
| 19-Nov-2025 15:24:35 | BUILD SUCCESSFUL in 4m 36s |
| 19-Nov-2025 15:24:35 | 32 actionable tasks: 31 executed, 1 up-to-date |
| 19-Nov-2025 15:24:36 | Finished task 'Jalview DEVELOP distribution for Java 11' with result: Success |
| 19-Nov-2025 15:24:36 | Starting task 'Create tar of DEVELOP channel installers' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' |
| 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)' ... running command line: /srv/bamboo/bamboo-home/temp/JB-GDI439-JOB1-1-ScriptBuildTask-3156143052934788813.sh ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=development/Release_2_11_5_Branch bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_planRepository_1_branchDisplayName=development/Release_2_11_5_Branch bamboo_repository_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDI439-JOB1 bamboo_repository_46498596_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortPlanName=development-Release_2_11_5_Branch bamboo_planRepository_name=Jalview Gitlab bamboo_repository_46498596_git_branch=development/Release_2_11_5_Branch bamboo_buildNumber=1 bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDI439-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch bamboo_shortPlanKey=GDI439 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_buildTimeStamp=2025-11-19T15:10:38.943Z bamboo_repository_git_branch=development/Release_2_11_5_Branch bamboo_buildResultKey=JB-GDI439-JOB1-1 bamboo_repository_branch_name=development/Release_2_11_5_Branch bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Installers - development-Release_2_11_5_Branch - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_repository_46498596_name=Jalview Gitlab bamboo_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 bamboo_dependenciesDisabled=false bamboo_repository_46498596_revision_number=b0fd08a15bfaff92e5d6c81412f82b5902ac284e bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=development/Release_2_11_5_Branch bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=development/Release_2_11_5_Branch bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=development/Release_2_11_5_Branch bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46302763 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=jprocter bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDI439-JOB1 bamboo_planKey=JB-GDI439 bamboo_repository_46498596_git_username= bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498596_branch_name=development/Release_2_11_5_Branch bamboo_planRepository_1_branchName=development/Release_2_11_5_Branch |
| 19-Nov-2025 15:24:36 | installers/ |
| 19-Nov-2025 15:24:36 | installers/tmp/ |
| 19-Nov-2025 15:24:36 | installers/tmp/default.vmoptions.AARCH64 |
| 19-Nov-2025 15:24:36 | installers/tmp/default.vmoptions.X64 |
| 19-Nov-2025 15:24:36 | installers/11/ |
| 19-Nov-2025 15:24:36 | installers/11/Jalview_Develop-2_11_5_1-d20251119-windows-x64-java_11.exe |
| 19-Nov-2025 15:24:40 | installers/11/jalview_develop-2_11_5_1-d20251119-unix-java_11.sh |
| 19-Nov-2025 15:24:41 | installers/11/sha256sums |
| 19-Nov-2025 15:24:41 | installers/11/md5sums |
| 19-Nov-2025 15:24:41 | installers/11/jalview_develop-2_11_5_1-d20251119-unix-java_11.tar.gz |
| 19-Nov-2025 15:24:43 | installers/11/output.txt |
| 19-Nov-2025 15:24:43 | installers/11/jalview_develop-2_11_5_1-d20251119-linux-x64-java_11.sh |
| 19-Nov-2025 15:24:46 | installers/11/Jalview_Develop-2_11_5_1-d20251119-macos-aarch64-java_11.dmg |
| 19-Nov-2025 15:24:50 | installers/11/jalview_develop-2_11_5_1-d20251119-linux-aarch64-java_11.sh |
| 19-Nov-2025 15:24:53 | installers/11/Jalview_Develop-2_11_5_1-d20251119-macos-x64-java_11.dmg |
| 19-Nov-2025 15:24:56 | installers/11/updates.xml |
| 19-Nov-2025 15:24:56 | Finished task 'Create tar of DEVELOP channel installers' with result: Success |
| 19-Nov-2025 15:24:56 | Running post build plugin 'NCover Results Collector' |
| 19-Nov-2025 15:24:56 | Running post build plugin 'Artifact Copier' |
| 19-Nov-2025 15:24:56 | Publishing an artifact: develop_installers_tar |
| 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 |
| 19-Nov-2025 15:24:58 | Running post build plugin 'Artifactory Release Management Staging' |
| 19-Nov-2025 15:24:58 | Running post build plugin 'Artifactory Build Info Copier' |
| 19-Nov-2025 15:24:58 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 19-Nov-2025 15:24:58 | Running post build plugin 'npm Cache Cleanup' |
| 19-Nov-2025 15:24:58 | Running post build plugin 'Clover Results Collector' |
| 19-Nov-2025 15:24:58 | Running post build plugin 'Docker Container Cleanup' |
| 19-Nov-2025 15:24:58 | Finalising the build... |
| 19-Nov-2025 15:24:58 | Stopping timer. |
| 19-Nov-2025 15:24:58 | Build JB-GDI439-JOB1-1 completed. |
| 19-Nov-2025 15:24:58 | Running on server: post build plugin 'NCover Results Collector' |
| 19-Nov-2025 15:24:58 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 19-Nov-2025 15:24:58 | Running on server: post build plugin 'Clover Delta Calculator' |
| 19-Nov-2025 15:24:58 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 19-Nov-2025 15:24:58 | All post build plugins have finished |
| 19-Nov-2025 15:24:58 | Generating build results summary... |
| 19-Nov-2025 15:24:58 | Saving build results to disk... |
| 19-Nov-2025 15:24:58 | Logging substituted variables... |
| 19-Nov-2025 15:24:58 | Indexing build results... |
| 19-Nov-2025 15:24:58 | Finished building JB-GDI439-JOB1-1. |