Build: #1 was successful
Job: Default Job was successful
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| 27-Nov-2025 17:35:16 | Build Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1) started building on agent Default Agent |
| 27-Nov-2025 17:35:16 | |
| 27-Nov-2025 17:35:16 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1 |
| 27-Nov-2025 17:35:16 | Executing build Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1) |
| 27-Nov-2025 17:35:16 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 27-Nov-2025 17:35:16 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1 |
| 27-Nov-2025 17:35:16 | Updating source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588 |
| 27-Nov-2025 17:35:16 | Fetching 'refs/heads/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 27-Nov-2025 17:35:16 | Checking out revision acbb7d39481e53918a63f69cd008b4f6bbd7a588. |
| 27-Nov-2025 17:35:16 | Creating local git repository in '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/.git'. |
| 27-Nov-2025 17:35:16 | Cloning into '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1'... |
| 27-Nov-2025 17:35:16 | done. |
| 27-Nov-2025 17:35:24 | Switched to a new branch 'bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus' |
| 27-Nov-2025 17:35:24 | Branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus set up to track remote branch bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus from origin. |
| 27-Nov-2025 17:35:24 | Updated source code to revision: acbb7d39481e53918a63f69cd008b4f6bbd7a588 |
| 27-Nov-2025 17:35:24 | Finished task 'Checkout Default Repository' with result: Success |
| 27-Nov-2025 17:35:24 | Running pre-build action: VCS Version Collector |
| 27-Nov-2025 17:35:24 | Running pre-build action: Artifactory Release Staging |
| 27-Nov-2025 17:35:24 | Substituting variable: ${bamboo.planKey} with JB-GPC654 |
| 27-Nov-2025 17:35:24 | Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 27-Nov-2025 17:35:24 | Bamboo Artifactory Plugin version: 2.6.2 |
| 27-Nov-2025 17:35:25 | Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC654 clean shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_dependency_parent_0=JB-GDB729-5 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_dependency_parent_total=1 bamboo_planRepository_1_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC654-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-GPC654-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GPC654-JOB1 bamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46498600_name=Jalview Gitlab bamboo_repository_46498600_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_shortPlanKey=GPC654 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_buildTimeStamp=2025-11-27T17:19:12.535Z bamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_buildResultKey=JB-GPC654-JOB1-1 bamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab 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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_46498600_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_planRepository_1_type=gitv2 bamboo_repository_46498600_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus _=/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_repository_46498600_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_plan_storageTag=plan-46302771 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-GPC654-JOB1 bamboo_planKey=JB-GPC654 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498600_git_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 27-Nov-2025 17:35:27 | |
| 27-Nov-2025 17:35:27 | > Configure project : |
| 27-Nov-2025 17:35:27 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 27-Nov-2025 17:35:27 | JALVIEW_VERSION is set to '2.11.5.1' |
| 27-Nov-2025 17:35:27 | HEADLESS BUILD |
| 27-Nov-2025 17:35:27 | J2S ENABLED |
| 27-Nov-2025 17:35:27 | Using a BUILD profile. |
| 27-Nov-2025 17:35:27 | eclipseDir exists |
| 27-Nov-2025 17:35:27 | |
| 27-Nov-2025 17:35:27 | > Task :clean |
| 27-Nov-2025 17:35:27 | > Task :cleanPackageDir UP-TO-DATE |
| 27-Nov-2025 17:35:27 | > Task :copyHelp |
| 27-Nov-2025 17:35:29 | > Task :buildIndices |
| 27-Nov-2025 17:35:29 | > Task :copyResources |
| 27-Nov-2025 17:35:29 | > Task :copyChannelResources |
| 27-Nov-2025 17:35:29 | |
| 27-Nov-2025 17:35:29 | > Task :createBuildProperties |
| 27-Nov-2025 17:35:29 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:35:29 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:29 | |
| 27-Nov-2025 17:35:29 | > Task :buildResources |
| 27-Nov-2025 17:35:29 | > Task :copyDocs |
| 27-Nov-2025 17:35:29 | |
| 27-Nov-2025 17:35:29 | > Task :convertMdFiles |
| 27-Nov-2025 17:35:29 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 27-Nov-2025 17:35:29 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 27-Nov-2025 17:35:29 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 27-Nov-2025 17:35:29 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/building.html |
| 27-Nov-2025 17:35:29 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 27-Nov-2025 17:35:31 | |
| 27-Nov-2025 17:35:31 | > Task :releasesTemplates |
| 27-Nov-2025 17:35:31 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:35:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:31 | Stripping rc/test/etc for 2_11_5_1 |
| 27-Nov-2025 17:35:31 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md |
| 27-Nov-2025 17:35:31 | |
| 27-Nov-2025 17:35:31 | > Task :prepare |
| 27-Nov-2025 17:35:32 | |
| 27-Nov-2025 17:35:32 | > Task :compileJava |
| 27-Nov-2025 17:35:32 | Setting target compatibility to 11 |
| 27-Nov-2025 17:35:39 | |
| 27-Nov-2025 17:35:39 | > Task :processResources |
| 27-Nov-2025 17:35:39 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:39 | |
| 27-Nov-2025 17:35:39 | > Task :classes |
| 27-Nov-2025 17:35:39 | Note: Some input files use or override a deprecated API. |
| 27-Nov-2025 17:35:39 | Note: Recompile with -Xlint:deprecation for details. |
| 27-Nov-2025 17:35:39 | Note: Some input files use unchecked or unsafe operations. |
| 27-Nov-2025 17:35:39 | Note: Recompile with -Xlint:unchecked for details. |
| 27-Nov-2025 17:35:41 | |
| 27-Nov-2025 17:35:41 | > Task :compileLinkCheck |
| 27-Nov-2025 17:35:41 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:35:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:41 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:35:45 | |
| 27-Nov-2025 17:35:45 | > Task :linkCheck |
| 27-Nov-2025 17:35:45 | Checking help file links |
| 27-Nov-2025 17:37:51 | |
| 27-Nov-2025 17:37:51 | Results: |
| 27-Nov-2025 17:37:51 | 161 distinct help targets |
| 27-Nov-2025 17:37:51 | 161 help mappings |
| 27-Nov-2025 17:37:51 | 0 invalid targets |
| 27-Nov-2025 17:37:51 | 31 unused targets |
| 27-Nov-2025 17:37:52 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 27-Nov-2025 17:37:52 | overviewprefs: html/features/preferences.html#overview |
| 27-Nov-2025 17:37:52 | cdnafeatures: html/features/codingfeatures.html |
| 27-Nov-2025 17:37:52 | startupprefs: html/features/preferences.html#startup |
| 27-Nov-2025 17:37:52 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 27-Nov-2025 17:37:52 | io.modellerpir: html/io/modellerpir.html |
| 27-Nov-2025 17:37:52 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 27-Nov-2025 17:37:52 | pdbmcviewer: html/features/pdbviewer.html |
| 27-Nov-2025 17:37:52 | groovy.colours: html/features/groovy.html#groovyColours |
| 27-Nov-2025 17:37:52 | seqmappings: html/features/seqmappings.html |
| 27-Nov-2025 17:37:52 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 27-Nov-2025 17:37:52 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 27-Nov-2025 17:37:52 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 27-Nov-2025 17:37:52 | search: html/features/search.html |
| 27-Nov-2025 17:37:52 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 27-Nov-2025 17:37:52 | alformats: html/io/fileformats.html |
| 27-Nov-2025 17:37:52 | strucprefs: html/features/preferences.html#structure |
| 27-Nov-2025 17:37:52 | siftsmapping: html/features/siftsmapping.html |
| 27-Nov-2025 17:37:52 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 27-Nov-2025 17:37:52 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 27-Nov-2025 17:37:52 | newkeys: html/features/newkeystrokes.html |
| 27-Nov-2025 17:37:52 | importvcf.attribs: html/features/importvcf.html#attribs |
| 27-Nov-2025 17:37:52 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 27-Nov-2025 17:37:52 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 27-Nov-2025 17:37:52 | jalarchive: html/features/jalarchive.html |
| 27-Nov-2025 17:37:52 | newsreader: html/webServices/newsreader.html |
| 27-Nov-2025 17:37:52 | jalviewcltool: html/features/commandline.html#script |
| 27-Nov-2025 17:37:52 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 27-Nov-2025 17:37:52 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 27-Nov-2025 17:37:52 | paematrixformat: html/io/paematrixformat.html |
| 27-Nov-2025 17:37:52 | overview: html/features/overview.html |
| 27-Nov-2025 17:37:52 | 0 invalid map urls |
| 27-Nov-2025 17:37:52 | 0 invalid image attributes |
| 27-Nov-2025 17:37:52 | 520 internal href links (120 with anchors) |
| 27-Nov-2025 17:37:52 | 0 invalid internal href links |
| 27-Nov-2025 17:37:52 | 0 invalid internal anchor links |
| 27-Nov-2025 17:37:52 | 112 external href links |
| 27-Nov-2025 17:37:52 | External links not verified as internet not available |
| 27-Nov-2025 17:37:52 | *** Success *** |
| 27-Nov-2025 17:37:53 | |
| 27-Nov-2025 17:37:53 | > Task :jar |
| 27-Nov-2025 17:37:53 | > Task :syncJars |
| 27-Nov-2025 17:37:53 | > Task :makeDist |
| 27-Nov-2025 17:38:02 | > Task :shadowJar |
| 27-Nov-2025 17:38:02 | |
| 27-Nov-2025 17:38:02 | > Task :getdownImagesCopy |
| 27-Nov-2025 17:38:02 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:38:02 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/utils/channels/default/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. |
| 27-Nov-2025 17:38:02 | |
| 27-Nov-2025 17:38:02 | > Task :getdownImagesProcess |
| 27-Nov-2025 17:38:02 | > Task :getdownImages |
| 27-Nov-2025 17:38:03 | > Task :getdownWebsiteBuild |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | > Task :getdownDigest |
| 27-Nov-2025 17:38:04 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 27-Nov-2025 17:38:04 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | > Task :getdown |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 27-Nov-2025 17:38:04 | Please consult deprecation warnings for more details. |
| 27-Nov-2025 17:38:04 | |
| 27-Nov-2025 17:38:04 | BUILD SUCCESSFUL in 2m 39s |
| 27-Nov-2025 17:38:04 | 22 actionable tasks: 21 executed, 1 up-to-date |
| 27-Nov-2025 17:38:04 | 2025/11/27 17:38:03:089 WARNING Starting without install4j classes |
| 27-Nov-2025 17:38:04 | 2025/11/27 17:38:04:041 WARNING Starting without install4j classes |
| 27-Nov-2025 17:38:05 | Finished task 'Jalview distribution for Java 11' with result: Success |
| 27-Nov-2025 17:38:05 | Substituting variable: ${bamboo.planKey} with JB-GPC654 |
| 27-Nov-2025 17:38:05 | Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 27-Nov-2025 17:38:05 | Bamboo Artifactory Plugin version: 2.6.2 |
| 27-Nov-2025 17:38:05 | Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job #1 (JB-GPC654-JOB1-1)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC654 shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_dependency_parent_0=JB-GDB729-5 bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_dependency_parent_total=1 bamboo_planRepository_1_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_repository_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC654-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-GPC654-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GPC654-JOB1 bamboo_shortPlanName=bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_planRepository_name=Jalview Gitlab LOGNAME=bamboo bamboo_buildNumber=1 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46498600_name=Jalview Gitlab bamboo_repository_46498600_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC654-JOB1-1 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_shortPlanKey=GPC654 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_buildTimeStamp=2025-11-27T17:19:12.535Z bamboo_repository_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_buildResultKey=JB-GPC654-JOB1-1 bamboo_repository_branch_name=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=acbb7d39481e53918a63f69cd008b4f6bbd7a588 SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab 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-GPC654 clean shadowJar getdown 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-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_46498600_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_planRepository_1_type=gitv2 bamboo_repository_46498600_revision_number=acbb7d39481e53918a63f69cd008b4f6bbd7a588 bamboo_planRepository_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus _=/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_repository_46498600_git_branch=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus bamboo_plan_storageTag=plan-46302771 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-GPC654-JOB1 bamboo_planKey=JB-GPC654 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498600_git_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 27-Nov-2025 17:38:06 | |
| 27-Nov-2025 17:38:06 | > Configure project : |
| 27-Nov-2025 17:38:06 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 27-Nov-2025 17:38:06 | JALVIEW_VERSION is set to '2.11.5.1' |
| 27-Nov-2025 17:38:06 | HEADLESS BUILD |
| 27-Nov-2025 17:38:06 | J2S ENABLED |
| 27-Nov-2025 17:38:06 | Using a BUILD profile. |
| 27-Nov-2025 17:38:06 | eclipseDir exists |
| 27-Nov-2025 17:38:06 | |
| 27-Nov-2025 17:38:06 | > Task :copyHelp UP-TO-DATE |
| 27-Nov-2025 17:38:07 | > Task :buildIndices |
| 27-Nov-2025 17:38:07 | > Task :copyResources UP-TO-DATE |
| 27-Nov-2025 17:38:07 | > Task :copyChannelResources UP-TO-DATE |
| 27-Nov-2025 17:38:07 | |
| 27-Nov-2025 17:38:07 | > Task :createBuildProperties |
| 27-Nov-2025 17:38:07 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:38:07 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:07 | |
| 27-Nov-2025 17:38:07 | > Task :buildResources |
| 27-Nov-2025 17:38:07 | > Task :copyDocs |
| 27-Nov-2025 17:38:07 | |
| 27-Nov-2025 17:38:07 | > Task :convertMdFiles |
| 27-Nov-2025 17:38:07 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 27-Nov-2025 17:38:07 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 27-Nov-2025 17:38:07 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 27-Nov-2025 17:38:07 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/building.html |
| 27-Nov-2025 17:38:07 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 27-Nov-2025 17:38:07 | |
| 27-Nov-2025 17:38:07 | > Task :releasesTemplates |
| 27-Nov-2025 17:38:07 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:38:07 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:07 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:07 | Stripping rc/test/etc for 2_11_5_1 |
| 27-Nov-2025 17:38:07 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md |
| 27-Nov-2025 17:38:07 | |
| 27-Nov-2025 17:38:07 | > Task :prepare |
| 27-Nov-2025 17:38:09 | |
| 27-Nov-2025 17:38:09 | > Task :compileJava |
| 27-Nov-2025 17:38:09 | Setting target compatibility to 1.8 |
| 27-Nov-2025 17:38:16 | Note: Some input files use or override a deprecated API. |
| 27-Nov-2025 17:38:16 | Note: Recompile with -Xlint:deprecation for details. |
| 27-Nov-2025 17:38:16 | Note: Some input files use unchecked or unsafe operations. |
| 27-Nov-2025 17:38:16 | Note: Recompile with -Xlint:unchecked for details. |
| 27-Nov-2025 17:38:20 | |
| 27-Nov-2025 17:38:20 | > Task :processResources |
| 27-Nov-2025 17:38:20 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:20 | |
| 27-Nov-2025 17:38:20 | > Task :classes |
| 27-Nov-2025 17:38:20 | > Task :cleanPackageDir |
| 27-Nov-2025 17:38:22 | |
| 27-Nov-2025 17:38:22 | > Task :compileLinkCheck |
| 27-Nov-2025 17:38:22 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:38:22 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:22 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-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. |
| 27-Nov-2025 17:38:24 | |
| 27-Nov-2025 17:38:24 | > Task :linkCheck |
| 27-Nov-2025 17:38:24 | Checking help file links |
| 27-Nov-2025 17:40:30 | |
| 27-Nov-2025 17:40:30 | Results: |
| 27-Nov-2025 17:40:30 | 161 distinct help targets |
| 27-Nov-2025 17:40:30 | 161 help mappings |
| 27-Nov-2025 17:40:30 | 0 invalid targets |
| 27-Nov-2025 17:40:30 | 31 unused targets |
| 27-Nov-2025 17:40:30 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 27-Nov-2025 17:40:30 | overviewprefs: html/features/preferences.html#overview |
| 27-Nov-2025 17:40:30 | cdnafeatures: html/features/codingfeatures.html |
| 27-Nov-2025 17:40:30 | startupprefs: html/features/preferences.html#startup |
| 27-Nov-2025 17:40:30 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 27-Nov-2025 17:40:30 | io.modellerpir: html/io/modellerpir.html |
| 27-Nov-2025 17:40:30 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 27-Nov-2025 17:40:30 | pdbmcviewer: html/features/pdbviewer.html |
| 27-Nov-2025 17:40:30 | groovy.colours: html/features/groovy.html#groovyColours |
| 27-Nov-2025 17:40:30 | seqmappings: html/features/seqmappings.html |
| 27-Nov-2025 17:40:30 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 27-Nov-2025 17:40:30 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 27-Nov-2025 17:40:30 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 27-Nov-2025 17:40:30 | search: html/features/search.html |
| 27-Nov-2025 17:40:30 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 27-Nov-2025 17:40:30 | alformats: html/io/fileformats.html |
| 27-Nov-2025 17:40:30 | strucprefs: html/features/preferences.html#structure |
| 27-Nov-2025 17:40:30 | siftsmapping: html/features/siftsmapping.html |
| 27-Nov-2025 17:40:30 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 27-Nov-2025 17:40:30 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 27-Nov-2025 17:40:30 | newkeys: html/features/newkeystrokes.html |
| 27-Nov-2025 17:40:30 | importvcf.attribs: html/features/importvcf.html#attribs |
| 27-Nov-2025 17:40:30 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 27-Nov-2025 17:40:30 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 27-Nov-2025 17:40:30 | jalarchive: html/features/jalarchive.html |
| 27-Nov-2025 17:40:30 | newsreader: html/webServices/newsreader.html |
| 27-Nov-2025 17:40:30 | jalviewcltool: html/features/commandline.html#script |
| 27-Nov-2025 17:40:30 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 27-Nov-2025 17:40:30 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 27-Nov-2025 17:40:30 | paematrixformat: html/io/paematrixformat.html |
| 27-Nov-2025 17:40:30 | overview: html/features/overview.html |
| 27-Nov-2025 17:40:30 | 0 invalid map urls |
| 27-Nov-2025 17:40:30 | 0 invalid image attributes |
| 27-Nov-2025 17:40:30 | 520 internal href links (120 with anchors) |
| 27-Nov-2025 17:40:30 | 0 invalid internal href links |
| 27-Nov-2025 17:40:30 | 0 invalid internal anchor links |
| 27-Nov-2025 17:40:30 | 112 external href links |
| 27-Nov-2025 17:40:30 | External links not verified as internet not available |
| 27-Nov-2025 17:40:30 | *** Success *** |
| 27-Nov-2025 17:40:30 | |
| 27-Nov-2025 17:40:30 | > Task :jar |
| 27-Nov-2025 17:40:31 | > Task :syncJars |
| 27-Nov-2025 17:40:31 | > Task :makeDist |
| 27-Nov-2025 17:40:38 | > Task :shadowJar |
| 27-Nov-2025 17:40:38 | |
| 27-Nov-2025 17:40:38 | > Task :getdownImagesCopy |
| 27-Nov-2025 17:40:38 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:40:38 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/utils/channels/default/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. |
| 27-Nov-2025 17:40:38 | |
| 27-Nov-2025 17:40:38 | > Task :getdownImagesProcess |
| 27-Nov-2025 17:40:38 | > Task :getdownImages |
| 27-Nov-2025 17:40:38 | > Task :getdownWebsiteBuild |
| 27-Nov-2025 17:40:40 | 2025/11/27 17:40:38:956 WARNING Starting without install4j classes |
| 27-Nov-2025 17:40:40 | 2025/11/27 17:40:39:448 WARNING Starting without install4j classes |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | > Task :getdownDigest |
| 27-Nov-2025 17:40:40 | Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'... |
| 27-Nov-2025 17:40:40 | Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'... |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | > Task :getdown |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 27-Nov-2025 17:40:40 | Please consult deprecation warnings for more details. |
| 27-Nov-2025 17:40:40 | |
| 27-Nov-2025 17:40:40 | BUILD SUCCESSFUL in 2m 35s |
| 27-Nov-2025 17:40:40 | 21 actionable tasks: 18 executed, 3 up-to-date |
| 27-Nov-2025 17:40:40 | Finished task 'Jalview distribution for Java 8' with result: Success |
| 27-Nov-2025 17:40:40 | Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled |
| 27-Nov-2025 17:40:40 | Running post build plugin 'NCover Results Collector' |
| 27-Nov-2025 17:40:40 | Running post build plugin 'Artifact Copier' |
| 27-Nov-2025 17:40:40 | Publishing an artifact: Jalview executables |
| 27-Nov-2025 17:40:41 | Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 216.3 ms |
| 27-Nov-2025 17:40:41 | Publishing an artifact: install4j installers |
| 27-Nov-2025 17:40:41 | Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/install4j does not exist. |
| 27-Nov-2025 17:40:41 | The artifact hasn't been successfully published after 4.264 ms |
| 27-Nov-2025 17:40:41 | Publishing an artifact: getdown-channel |
| 27-Nov-2025 17:40:41 | Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/getdown/website does not exist. |
| 27-Nov-2025 17:40:41 | The artifact hasn't been successfully published after 178.9 μs |
| 27-Nov-2025 17:40:41 | Publishing an artifact: Jalview getdown launcher |
| 27-Nov-2025 17:40:41 | Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/getdown/files does not exist. |
| 27-Nov-2025 17:40:41 | The artifact hasn't been successfully published after 46.39 μs |
| 27-Nov-2025 17:40:41 | Publishing an artifact: getdown build for website |
| 27-Nov-2025 17:40:42 | Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 1.130 s |
| 27-Nov-2025 17:40:42 | Publishing an artifact: getdown build for archive |
| 27-Nov-2025 17:40:42 | Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC654-JOB1/build/website/docroot/old does not exist. |
| 27-Nov-2025 17:40:42 | The artifact hasn't been successfully published after 152.2 μs |
| 27-Nov-2025 17:40:42 | Running post build plugin 'Artifactory Release Management Staging' |
| 27-Nov-2025 17:40:42 | Running post build plugin 'Artifactory Build Info Copier' |
| 27-Nov-2025 17:40:42 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 27-Nov-2025 17:40:42 | Running post build plugin 'npm Cache Cleanup' |
| 27-Nov-2025 17:40:42 | Running post build plugin 'Clover Results Collector' |
| 27-Nov-2025 17:40:42 | Running post build plugin 'Docker Container Cleanup' |
| 27-Nov-2025 17:40:42 | Finalising the build... |
| 27-Nov-2025 17:40:42 | Stopping timer. |
| 27-Nov-2025 17:40:42 | Build JB-GPC654-JOB1-1 completed. |
| 27-Nov-2025 17:40:42 | Running on server: post build plugin 'NCover Results Collector' |
| 27-Nov-2025 17:40:42 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 27-Nov-2025 17:40:42 | Running on server: post build plugin 'Clover Delta Calculator' |
| 27-Nov-2025 17:40:42 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 27-Nov-2025 17:40:42 | All post build plugins have finished |
| 27-Nov-2025 17:40:42 | Generating build results summary... |
| 27-Nov-2025 17:40:42 | Saving build results to disk... |
| 27-Nov-2025 17:40:42 | Logging substituted variables... |
| 27-Nov-2025 17:40:42 | Indexing build results... |
| 27-Nov-2025 17:40:42 | Finished building JB-GPC654-JOB1-1. |