Build: #3 was successful
Job: Default Job was successful
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| 19-Feb-2026 11:24:59 | Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #3 (JB-GDL123-JOB1-3) started building on agent Default Agent |
| 19-Feb-2026 11:24:59 | |
| 19-Feb-2026 11:24:59 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 |
| 19-Feb-2026 11:24:59 | Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #3 (JB-GDL123-JOB1-3) |
| 19-Feb-2026 11:24:59 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 19-Feb-2026 11:24:59 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 |
| 19-Feb-2026 11:24:59 | Updating source code to revision: 944aa492571e8adede487266d9a4a7143a7cc0df |
| 19-Feb-2026 11:24:59 | Fetching 'refs/heads/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 19-Feb-2026 11:24:59 | Checking out revision 944aa492571e8adede487266d9a4a7143a7cc0df. |
| 19-Feb-2026 11:24:59 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 19-Feb-2026 11:24:59 | dbbef33..944aa49 bug/JAL-4624_JAL-4623_Mul_SS_in_PCA -> origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA |
| 19-Feb-2026 11:24:59 | ab2dfae..1617d0e citation.cff -> origin/citation.cff |
| 19-Feb-2026 11:24:59 | 65ba1d2..9efd725 epic/JAL-4320_gradle_upgrade_to_gradle9 -> origin/epic/JAL-4320_gradle_upgrade_to_gradle9 |
| 19-Feb-2026 11:24:59 | 87afc89..42e19e3 main -> origin/main |
| 19-Feb-2026 11:24:59 | * [new tag] Release_2_11_5_1 -> Release_2_11_5_1 |
| 19-Feb-2026 11:24:59 | Already on 'bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' |
| 19-Feb-2026 11:24:59 | Your branch is behind 'origin/bug/JAL-4624_JAL-4623_Mul_SS_in_PCA' by 1 commit, and can be fast-forwarded. |
| 19-Feb-2026 11:24:59 | (use "git pull" to update your local branch) |
| 19-Feb-2026 11:25:00 | HEAD is now at 944aa49 JAL-4623 Changes for PCA (Annotation based) |
| 19-Feb-2026 11:25:00 | Updated source code to revision: 944aa492571e8adede487266d9a4a7143a7cc0df |
| 19-Feb-2026 11:25:00 | Finished task 'Checkout Default Repository' with result: Success |
| 19-Feb-2026 11:25:00 | Running pre-build action: VCS Version Collector |
| 19-Feb-2026 11:25:00 | Running pre-build action: Artifactory Release Staging |
| 19-Feb-2026 11:25:00 | Substituting variable: ${bamboo.planKey} with JB-GDL123 |
| 19-Feb-2026 11:25:00 | Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 19-Feb-2026 11:25:00 | Bamboo Artifactory Plugin version: 2.6.2 |
| 19-Feb-2026 11:25:00 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #3 (JB-GDL123-JOB1-3)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL123 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_dependency_parent_0=JB-GDB744-4 bamboo_repository_48169016_previous_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_dependency_parent_total=1 bamboo_repository_48169016_name=Jalview Gitlab bamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_repository_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-3 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-GDL123-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDL123-JOB1 bamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=3 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169016_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_shortPlanKey=GDL123 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_buildTimeStamp=2026-02-19T11:24:59.010Z bamboo_repository_previous_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382 bamboo_repository_48169016_git_username= bamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_buildResultKey=JB-GDL123-JOB1-3 bamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_repository_48169016_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_1_revision=944aa492571e8adede487266d9a4a7143a7cc0df SHLVL=1 bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_48169016_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_repository_name=Jalview Gitlab bamboo_repository_48169016_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ 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=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA 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=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA _=/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-47972463 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_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-GDL123-JOB1 bamboo_planKey=JB-GDL123 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 19-Feb-2026 11:25:02 | |
| 19-Feb-2026 11:25:02 | > Configure project : |
| 19-Feb-2026 11:25:02 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 19-Feb-2026 11:25:02 | JALVIEW_VERSION is set to '2.12.0' |
| 19-Feb-2026 11:25:02 | HEADLESS BUILD |
| 19-Feb-2026 11:25:02 | J2S ENABLED |
| 19-Feb-2026 11:25:02 | Using a BUILD profile. |
| 19-Feb-2026 11:25:02 | eclipseDir exists |
| 19-Feb-2026 11:25:02 | |
| 19-Feb-2026 11:25:02 | > Task :clean |
| 19-Feb-2026 11:25:02 | > Task :cleanPackageDir |
| 19-Feb-2026 11:25:02 | > Task :getdownImagesCopy |
| 19-Feb-2026 11:25:02 | > Task :getdownImagesProcess |
| 19-Feb-2026 11:25:02 | > Task :getdownImages |
| 19-Feb-2026 11:25:03 | > Task :copyHelp |
| 19-Feb-2026 11:25:04 | > Task :buildIndices |
| 19-Feb-2026 11:25:04 | > Task :copyResources |
| 19-Feb-2026 11:25:04 | > Task :copyChannelResources |
| 19-Feb-2026 11:25:04 | |
| 19-Feb-2026 11:25:04 | > Task :createBuildProperties |
| 19-Feb-2026 11:25:04 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 19-Feb-2026 11:25:04 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:04 | |
| 19-Feb-2026 11:25:04 | > Task :buildResources |
| 19-Feb-2026 11:25:04 | > Task :copyDocs |
| 19-Feb-2026 11:25:04 | |
| 19-Feb-2026 11:25:04 | > Task :convertMdFiles |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/JalviewJS-API.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/building.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/addingWebClient.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 19-Feb-2026 11:25:04 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build/doc/JalviewJS-startupParams.html |
| 19-Feb-2026 11:25:05 | |
| 19-Feb-2026 11:25:05 | > Task :releasesTemplates |
| 19-Feb-2026 11:25:05 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 19-Feb-2026 11:25:05 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:05 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:05 | Stripping rc/test/etc for 2_12_0 |
| 19-Feb-2026 11:25:05 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/help/markdown/whatsnew/whatsnew-2_12_0.md |
| 19-Feb-2026 11:25:05 | |
| 19-Feb-2026 11:25:05 | > Task :prepare |
| 19-Feb-2026 11:25:07 | |
| 19-Feb-2026 11:25:07 | > Task :compileJava |
| 19-Feb-2026 11:25:07 | Setting target compatibility to 11 |
| 19-Feb-2026 11:25:13 | Note: Some input files use or override a deprecated API. |
| 19-Feb-2026 11:25:13 | Note: Recompile with -Xlint:deprecation for details. |
| 19-Feb-2026 11:25:13 | Note: Some input files use unchecked or unsafe operations. |
| 19-Feb-2026 11:25:13 | Note: Recompile with -Xlint:unchecked for details. |
| 19-Feb-2026 11:25:13 | |
| 19-Feb-2026 11:25:13 | > Task :processResources |
| 19-Feb-2026 11:25:13 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 19-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 19-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:13 | |
| 19-Feb-2026 11:25:13 | > Task :classes |
| 19-Feb-2026 11:25:14 | |
| 19-Feb-2026 11:25:14 | > Task :compileLinkCheck |
| 19-Feb-2026 11:25:14 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 19-Feb-2026 11:25:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-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-Feb-2026 11:25:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 19-Feb-2026 11:25:15 | |
| 19-Feb-2026 11:25:15 | > Task :linkCheck |
| 19-Feb-2026 11:25:15 | Checking help file links |
| 19-Feb-2026 11:25:15 | |
| 19-Feb-2026 11:25:15 | Results: |
| 19-Feb-2026 11:25:15 | 162 distinct help targets |
| 19-Feb-2026 11:25:15 | 162 help mappings |
| 19-Feb-2026 11:25:15 | 0 invalid targets |
| 19-Feb-2026 11:25:15 | 31 unused targets |
| 19-Feb-2026 11:25:15 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 19-Feb-2026 11:25:15 | overviewprefs: html/features/preferences.html#overview |
| 19-Feb-2026 11:25:15 | cdnafeatures: html/features/codingfeatures.html |
| 19-Feb-2026 11:25:15 | startupprefs: html/features/preferences.html#startup |
| 19-Feb-2026 11:25:15 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 19-Feb-2026 11:25:15 | io.modellerpir: html/io/modellerpir.html |
| 19-Feb-2026 11:25:15 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 19-Feb-2026 11:25:15 | pdbmcviewer: html/features/pdbviewer.html |
| 19-Feb-2026 11:25:15 | groovy.colours: html/features/groovy.html#groovyColours |
| 19-Feb-2026 11:25:15 | seqmappings: html/features/seqmappings.html |
| 19-Feb-2026 11:25:15 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 19-Feb-2026 11:25:15 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 19-Feb-2026 11:25:15 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 19-Feb-2026 11:25:15 | search: html/features/search.html |
| 19-Feb-2026 11:25:15 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 19-Feb-2026 11:25:15 | alformats: html/io/fileformats.html |
| 19-Feb-2026 11:25:15 | strucprefs: html/features/preferences.html#structure |
| 19-Feb-2026 11:25:15 | siftsmapping: html/features/siftsmapping.html |
| 19-Feb-2026 11:25:15 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 19-Feb-2026 11:25:15 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 19-Feb-2026 11:25:15 | newkeys: html/features/newkeystrokes.html |
| 19-Feb-2026 11:25:15 | importvcf.attribs: html/features/importvcf.html#attribs |
| 19-Feb-2026 11:25:15 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 19-Feb-2026 11:25:15 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 19-Feb-2026 11:25:15 | jalarchive: html/features/jalarchive.html |
| 19-Feb-2026 11:25:15 | newsreader: html/webServices/newsreader.html |
| 19-Feb-2026 11:25:15 | jalviewcltool: html/features/commandline.html#script |
| 19-Feb-2026 11:25:15 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 19-Feb-2026 11:25:15 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 19-Feb-2026 11:25:15 | paematrixformat: html/io/paematrixformat.html |
| 19-Feb-2026 11:25:15 | overview: html/features/overview.html |
| 19-Feb-2026 11:25:15 | 0 invalid map urls |
| 19-Feb-2026 11:25:15 | 0 invalid image attributes |
| 19-Feb-2026 11:25:15 | 520 internal href links (119 with anchors) |
| 19-Feb-2026 11:25:15 | 0 invalid internal href links |
| 19-Feb-2026 11:25:15 | 0 invalid internal anchor links |
| 19-Feb-2026 11:25:15 | 113 external href links |
| 19-Feb-2026 11:25:15 | External links not verified as internet not available |
| 19-Feb-2026 11:25:15 | *** Success *** |
| 19-Feb-2026 11:25:15 | |
| 19-Feb-2026 11:25:15 | > Task :jar |
| 19-Feb-2026 11:25:16 | > Task :syncJars |
| 19-Feb-2026 11:25:16 | > Task :makeDist |
| 19-Feb-2026 11:25:16 | > Task :getdownWebsiteBuild |
| 19-Feb-2026 11:25:18 | 2026/02/19 11:25:16:855 WARNING Starting without install4j classes |
| 19-Feb-2026 11:25:18 | 2026/02/19 11:25:17:443 WARNING Starting without install4j classes |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | > Task :getdownDigest |
| 19-Feb-2026 11:25:18 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 19-Feb-2026 11:25:18 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | > Task :getdown |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. |
| 19-Feb-2026 11:25:18 | Please consult deprecation warnings for more details. |
| 19-Feb-2026 11:25:18 | |
| 19-Feb-2026 11:25:18 | BUILD SUCCESSFUL in 17s |
| 19-Feb-2026 11:25:18 | 21 actionable tasks: 21 executed |
| 19-Feb-2026 11:25:18 | Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success |
| 19-Feb-2026 11:25:18 | Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' |
| 19-Feb-2026 11:25:18 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job #3 (JB-GDL123-JOB1-3)' ... running command line: /srv/bamboo/bamboo-home/temp/JB-GDL123-JOB1-3-ScriptBuildTask-3648935088025890098.sh ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_dependency_parent_0=JB-GDB744-4 bamboo_repository_48169016_previous_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_dependency_parent_total=1 bamboo_repository_48169016_name=Jalview Gitlab bamboo_planRepository_1_branchDisplayName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_repository_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-3 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL123-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDL123-JOB1 bamboo_shortPlanName=bug-JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_name=Jalview Gitlab bamboo_buildNumber=3 bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_48169016_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL123-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_shortPlanKey=GDL123 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_buildTimeStamp=2026-02-19T11:24:59.010Z bamboo_repository_previous_revision_number=dbbef339de0089e00e1a460dd6f099e671ff9382 bamboo_repository_48169016_git_username= bamboo_repository_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_buildResultKey=JB-GDL123-JOB1-3 bamboo_repository_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4624_JAL-4623_Mul_SS_in_PCA - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_repository_48169016_branch_name=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_1_revision=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_48169016_git_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_repository_name=Jalview Gitlab bamboo_repository_48169016_revision_number=944aa492571e8adede487266d9a4a7143a7cc0df bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL123 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA 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=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA 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-47972463 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_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-GDL123-JOB1 bamboo_planKey=JB-GDL123 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_planRepository_1_branchName=bug/JAL-4624_JAL-4623_Mul_SS_in_PCA |
| 19-Feb-2026 11:25:18 | Finished task 'Copy JVL file and produce link in HTML' with result: Success |
| 19-Feb-2026 11:25:18 | Running post build plugin 'NCover Results Collector' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Artifact Copier' |
| 19-Feb-2026 11:25:18 | Publishing an artifact: getdown |
| 19-Feb-2026 11:25:18 | Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 143.7 ms |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Artifactory Release Management Staging' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Artifactory Build Info Copier' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'npm Cache Cleanup' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Clover Results Collector' |
| 19-Feb-2026 11:25:18 | Running post build plugin 'Docker Container Cleanup' |
| 19-Feb-2026 11:25:18 | Finalising the build... |
| 19-Feb-2026 11:25:18 | Stopping timer. |
| 19-Feb-2026 11:25:18 | Build JB-GDL123-JOB1-3 completed. |
| 19-Feb-2026 11:25:18 | Running on server: post build plugin 'NCover Results Collector' |
| 19-Feb-2026 11:25:18 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 19-Feb-2026 11:25:18 | Running on server: post build plugin 'Clover Delta Calculator' |
| 19-Feb-2026 11:25:18 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 19-Feb-2026 11:25:18 | All post build plugins have finished |
| 19-Feb-2026 11:25:18 | Generating build results summary... |
| 19-Feb-2026 11:25:18 | Saving build results to disk... |
| 19-Feb-2026 11:25:18 | Logging substituted variables... |
| 19-Feb-2026 11:25:18 | Indexing build results... |
| 19-Feb-2026 11:25:18 | Finished building JB-GDL123-JOB1-3. |