Build: #3 was successful
Job: Default Job was successful
Build log
The build generated 354 lines of output. Download or view full build log
| 28-Nov-2025 18:00:29 | Build Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GPC652-JOB1-3) started building on agent Default Agent |
| 28-Nov-2025 18:00:29 | |
| 28-Nov-2025 18:00:29 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1 |
| 28-Nov-2025 18:00:30 | Executing build Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GPC652-JOB1-3) |
| 28-Nov-2025 18:00:30 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 28-Nov-2025 18:00:30 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1 |
| 28-Nov-2025 18:00:30 | Updating source code to revision: 6f2c311824a96fc172e1713db11e8c1cdb24e48c |
| 28-Nov-2025 18:00:30 | Fetching 'refs/heads/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 28-Nov-2025 18:00:30 | Checking out revision 6f2c311824a96fc172e1713db11e8c1cdb24e48c. |
| 28-Nov-2025 18:00:31 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 28-Nov-2025 18:00:31 | c0746f1..6f2c311 bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest |
| 28-Nov-2025 18:00:31 | Already on 'bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' |
| 28-Nov-2025 18:00:31 | Your branch is behind 'origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' by 3 commits, and can be fast-forwarded. |
| 28-Nov-2025 18:00:31 | (use "git pull" to update your local branch) |
| 28-Nov-2025 18:00:31 | HEAD is now at 6f2c311 JAL-4633 attempted workaround - really need a j2stest to verify that the j2s-ed expression is correct. |
| 28-Nov-2025 18:00:31 | Updated source code to revision: 6f2c311824a96fc172e1713db11e8c1cdb24e48c |
| 28-Nov-2025 18:00:31 | Finished task 'Checkout Default Repository' with result: Success |
| 28-Nov-2025 18:00:31 | Running pre-build action: VCS Version Collector |
| 28-Nov-2025 18:00:31 | Running pre-build action: Artifactory Release Staging |
| 28-Nov-2025 18:00:31 | Substituting variable: ${bamboo.planKey} with JB-GPC652 |
| 28-Nov-2025 18:00:31 | Starting task 'Jalview distribution for Java 11' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 28-Nov-2025 18:00:31 | Bamboo Artifactory Plugin version: 2.6.2 |
| 28-Nov-2025 18:00:31 | Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GPC652-JOB1-3)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GPC652 clean shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_dependency_parent_0=JB-GDB727-4 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC652-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-GPC652-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GPC652-JOB1 bamboo_repository_46498586_git_username= bamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest 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_46498586_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC652-JOB1-3 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_shortPlanKey=GPC652 bamboo_repository_46498586_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_repository_46498586_name=Jalview Gitlab bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_buildTimeStamp=2025-11-28T18:00:29.681Z bamboo_repository_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_repository_46498586_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildResultKey=JB-GPC652-JOB1-3 bamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_repository_46498586_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest _=/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-46302743 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-GPC652-JOB1 bamboo_planKey=JB-GPC652 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498586_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 28-Nov-2025 18:00:34 | |
| 28-Nov-2025 18:00:34 | > Configure project : |
| 28-Nov-2025 18:00:34 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 28-Nov-2025 18:00:34 | JALVIEW_VERSION is set to '2.11.5.1' |
| 28-Nov-2025 18:00:34 | HEADLESS BUILD |
| 28-Nov-2025 18:00:34 | J2S ENABLED |
| 28-Nov-2025 18:00:34 | Using a BUILD profile. |
| 28-Nov-2025 18:00:34 | eclipseDir exists |
| 28-Nov-2025 18:00:35 | |
| 28-Nov-2025 18:00:35 | > Task :clean |
| 28-Nov-2025 18:00:35 | > Task :cleanPackageDir |
| 28-Nov-2025 18:00:35 | > Task :copyHelp |
| 28-Nov-2025 18:00:37 | > Task :buildIndices |
| 28-Nov-2025 18:00:37 | > Task :copyResources |
| 28-Nov-2025 18:00:37 | > Task :copyChannelResources |
| 28-Nov-2025 18:00:37 | |
| 28-Nov-2025 18:00:37 | > Task :createBuildProperties |
| 28-Nov-2025 18:00:37 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:00:37 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:37 | |
| 28-Nov-2025 18:00:37 | > Task :buildResources |
| 28-Nov-2025 18:00:37 | > Task :copyDocs |
| 28-Nov-2025 18:00:37 | |
| 28-Nov-2025 18:00:37 | > Task :convertMdFiles |
| 28-Nov-2025 18:00:37 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 28-Nov-2025 18:00:37 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 28-Nov-2025 18:00:37 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 28-Nov-2025 18:00:37 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/building.html |
| 28-Nov-2025 18:00:37 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 28-Nov-2025 18:00:37 | |
| 28-Nov-2025 18:00:37 | > Task :releasesTemplates |
| 28-Nov-2025 18:00:37 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:00:37 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:37 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:37 | Stripping rc/test/etc for 2_11_5_1 |
| 28-Nov-2025 18:00:37 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md |
| 28-Nov-2025 18:00:37 | |
| 28-Nov-2025 18:00:37 | > Task :prepare |
| 28-Nov-2025 18:00:39 | |
| 28-Nov-2025 18:00:39 | > Task :compileJava |
| 28-Nov-2025 18:00:39 | Setting target compatibility to 11 |
| 28-Nov-2025 18:00:46 | Note: Some input files use or override a deprecated API. |
| 28-Nov-2025 18:00:46 | Note: Recompile with -Xlint:deprecation for details. |
| 28-Nov-2025 18:00:46 | Note: Some input files use unchecked or unsafe operations. |
| 28-Nov-2025 18:00:46 | Note: Recompile with -Xlint:unchecked for details. |
| 28-Nov-2025 18:00:47 | |
| 28-Nov-2025 18:00:47 | > Task :processResources |
| 28-Nov-2025 18:00:47 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:47 | |
| 28-Nov-2025 18:00:47 | > Task :classes |
| 28-Nov-2025 18:00:49 | |
| 28-Nov-2025 18:00:49 | > Task :compileLinkCheck |
| 28-Nov-2025 18:00:49 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:00:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:00:51 | |
| 28-Nov-2025 18:00:51 | > Task :linkCheck |
| 28-Nov-2025 18:00:51 | Checking help file links |
| 28-Nov-2025 18:02:56 | |
| 28-Nov-2025 18:02:56 | Results: |
| 28-Nov-2025 18:02:56 | 161 distinct help targets |
| 28-Nov-2025 18:02:56 | 161 help mappings |
| 28-Nov-2025 18:02:56 | 0 invalid targets |
| 28-Nov-2025 18:02:56 | 31 unused targets |
| 28-Nov-2025 18:02:57 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 28-Nov-2025 18:02:57 | overviewprefs: html/features/preferences.html#overview |
| 28-Nov-2025 18:02:57 | cdnafeatures: html/features/codingfeatures.html |
| 28-Nov-2025 18:02:57 | startupprefs: html/features/preferences.html#startup |
| 28-Nov-2025 18:02:57 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 28-Nov-2025 18:02:57 | io.modellerpir: html/io/modellerpir.html |
| 28-Nov-2025 18:02:57 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 28-Nov-2025 18:02:57 | pdbmcviewer: html/features/pdbviewer.html |
| 28-Nov-2025 18:02:57 | groovy.colours: html/features/groovy.html#groovyColours |
| 28-Nov-2025 18:02:57 | seqmappings: html/features/seqmappings.html |
| 28-Nov-2025 18:02:57 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 28-Nov-2025 18:02:57 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 28-Nov-2025 18:02:57 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 28-Nov-2025 18:02:57 | search: html/features/search.html |
| 28-Nov-2025 18:02:57 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 28-Nov-2025 18:02:57 | alformats: html/io/fileformats.html |
| 28-Nov-2025 18:02:57 | strucprefs: html/features/preferences.html#structure |
| 28-Nov-2025 18:02:57 | siftsmapping: html/features/siftsmapping.html |
| 28-Nov-2025 18:02:57 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 28-Nov-2025 18:02:57 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 28-Nov-2025 18:02:57 | newkeys: html/features/newkeystrokes.html |
| 28-Nov-2025 18:02:57 | importvcf.attribs: html/features/importvcf.html#attribs |
| 28-Nov-2025 18:02:57 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 28-Nov-2025 18:02:57 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 28-Nov-2025 18:02:57 | jalarchive: html/features/jalarchive.html |
| 28-Nov-2025 18:02:57 | newsreader: html/webServices/newsreader.html |
| 28-Nov-2025 18:02:57 | jalviewcltool: html/features/commandline.html#script |
| 28-Nov-2025 18:02:57 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 28-Nov-2025 18:02:57 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 28-Nov-2025 18:02:57 | paematrixformat: html/io/paematrixformat.html |
| 28-Nov-2025 18:02:57 | overview: html/features/overview.html |
| 28-Nov-2025 18:02:57 | 0 invalid map urls |
| 28-Nov-2025 18:02:57 | 0 invalid image attributes |
| 28-Nov-2025 18:02:57 | 520 internal href links (120 with anchors) |
| 28-Nov-2025 18:02:57 | 0 invalid internal href links |
| 28-Nov-2025 18:02:57 | 0 invalid internal anchor links |
| 28-Nov-2025 18:02:57 | 112 external href links |
| 28-Nov-2025 18:02:57 | External links not verified as internet not available |
| 28-Nov-2025 18:02:57 | *** Success *** |
| 28-Nov-2025 18:02:57 | |
| 28-Nov-2025 18:02:57 | > Task :jar |
| 28-Nov-2025 18:02:58 | > Task :syncJars |
| 28-Nov-2025 18:02:58 | > Task :makeDist |
| 28-Nov-2025 18:03:07 | > Task :shadowJar |
| 28-Nov-2025 18:03:07 | |
| 28-Nov-2025 18:03:07 | > Task :getdownImagesCopy |
| 28-Nov-2025 18:03:07 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:03:07 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:07 | |
| 28-Nov-2025 18:03:07 | > Task :getdownImagesProcess |
| 28-Nov-2025 18:03:07 | > Task :getdownImages |
| 28-Nov-2025 18:03:08 | > Task :getdownWebsiteBuild |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | > Task :getdownDigest |
| 28-Nov-2025 18:03:09 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 28-Nov-2025 18:03:09 | 2025/11/28 18:03:08:211 WARNING Starting without install4j classes |
| 28-Nov-2025 18:03:09 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | > Task :getdown |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | 2025/11/28 18:03:09:246 WARNING Starting without install4j classes |
| 28-Nov-2025 18:03:09 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 28-Nov-2025 18:03:09 | Please consult deprecation warnings for more details. |
| 28-Nov-2025 18:03:09 | |
| 28-Nov-2025 18:03:09 | BUILD SUCCESSFUL in 2m 37s |
| 28-Nov-2025 18:03:09 | 22 actionable tasks: 22 executed |
| 28-Nov-2025 18:03:10 | Finished task 'Jalview distribution for Java 11' with result: Success |
| 28-Nov-2025 18:03:10 | Substituting variable: ${bamboo.planKey} with JB-GPC652 |
| 28-Nov-2025 18:03:10 | Starting task 'Jalview distribution for Java 8' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 28-Nov-2025 18:03:10 | Bamboo Artifactory Plugin version: 2.6.2 |
| 28-Nov-2025 18:03:10 | Beginning to execute external process for build 'Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GPC652-JOB1-3)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -x clean -PCHANNEL=BUILD -PJAVA_VERSION=1.8 -Pbamboo_planKey=JB-GPC652 shadowJar getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_dependency_parent_0=JB-GDB727-4 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GPC652-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-GPC652-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GPC652-JOB1 bamboo_repository_46498586_git_username= bamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest 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_46498586_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GPC652-JOB1-3 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_shortPlanKey=GPC652 bamboo_repository_46498586_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_repository_46498586_name=Jalview Gitlab bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_buildTimeStamp=2025-11-28T18:00:29.681Z bamboo_repository_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_repository_46498586_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c bamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildResultKey=JB-GPC652-JOB1-3 bamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildPlanName=Jalview Builds - Getdown Plan Channel - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c 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-GPC652 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-4581_jalviewjs_support_for_java_security_messagedigest bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_repository_46498586_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest _=/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-46302743 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-GPC652-JOB1 bamboo_planKey=JB-GPC652 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498586_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 28-Nov-2025 18:03:12 | |
| 28-Nov-2025 18:03:12 | > Configure project : |
| 28-Nov-2025 18:03:12 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 28-Nov-2025 18:03:12 | JALVIEW_VERSION is set to '2.11.5.1' |
| 28-Nov-2025 18:03:12 | HEADLESS BUILD |
| 28-Nov-2025 18:03:12 | J2S ENABLED |
| 28-Nov-2025 18:03:12 | Using a BUILD profile. |
| 28-Nov-2025 18:03:12 | eclipseDir exists |
| 28-Nov-2025 18:03:12 | |
| 28-Nov-2025 18:03:12 | > Task :copyHelp UP-TO-DATE |
| 28-Nov-2025 18:03:14 | > Task :buildIndices |
| 28-Nov-2025 18:03:14 | > Task :copyResources UP-TO-DATE |
| 28-Nov-2025 18:03:14 | > Task :copyChannelResources UP-TO-DATE |
| 28-Nov-2025 18:03:14 | |
| 28-Nov-2025 18:03:14 | > Task :createBuildProperties |
| 28-Nov-2025 18:03:14 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:03:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:14 | |
| 28-Nov-2025 18:03:14 | > Task :buildResources |
| 28-Nov-2025 18:03:14 | > Task :copyDocs |
| 28-Nov-2025 18:03:14 | |
| 28-Nov-2025 18:03:14 | > Task :convertMdFiles |
| 28-Nov-2025 18:03:14 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 28-Nov-2025 18:03:14 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 28-Nov-2025 18:03:14 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 28-Nov-2025 18:03:14 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/building.html |
| 28-Nov-2025 18:03:14 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 28-Nov-2025 18:03:14 | |
| 28-Nov-2025 18:03:14 | > Task :releasesTemplates |
| 28-Nov-2025 18:03:14 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:03:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:14 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:14 | Stripping rc/test/etc for 2_11_5_1 |
| 28-Nov-2025 18:03:14 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md |
| 28-Nov-2025 18:03:14 | |
| 28-Nov-2025 18:03:14 | > Task :prepare |
| 28-Nov-2025 18:03:17 | |
| 28-Nov-2025 18:03:17 | > Task :compileJava |
| 28-Nov-2025 18:03:17 | Setting target compatibility to 1.8 |
| 28-Nov-2025 18:03:23 | Note: Some input files use or override a deprecated API. |
| 28-Nov-2025 18:03:23 | Note: Recompile with -Xlint:deprecation for details. |
| 28-Nov-2025 18:03:23 | Note: Some input files use unchecked or unsafe operations. |
| 28-Nov-2025 18:03:23 | Note: Recompile with -Xlint:unchecked for details. |
| 28-Nov-2025 18:03:26 | |
| 28-Nov-2025 18:03:26 | > Task :processResources |
| 28-Nov-2025 18:03:26 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:26 | |
| 28-Nov-2025 18:03:26 | > Task :classes |
| 28-Nov-2025 18:03:26 | > Task :cleanPackageDir |
| 28-Nov-2025 18:03:28 | |
| 28-Nov-2025 18:03:28 | > Task :compileLinkCheck |
| 28-Nov-2025 18:03:28 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:03:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:28 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:03:30 | |
| 28-Nov-2025 18:03:30 | > Task :linkCheck |
| 28-Nov-2025 18:03:30 | Checking help file links |
| 28-Nov-2025 18:05:35 | |
| 28-Nov-2025 18:05:35 | Results: |
| 28-Nov-2025 18:05:35 | 161 distinct help targets |
| 28-Nov-2025 18:05:35 | 161 help mappings |
| 28-Nov-2025 18:05:35 | 0 invalid targets |
| 28-Nov-2025 18:05:35 | 31 unused targets |
| 28-Nov-2025 18:05:35 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 28-Nov-2025 18:05:35 | overviewprefs: html/features/preferences.html#overview |
| 28-Nov-2025 18:05:35 | cdnafeatures: html/features/codingfeatures.html |
| 28-Nov-2025 18:05:35 | startupprefs: html/features/preferences.html#startup |
| 28-Nov-2025 18:05:35 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 28-Nov-2025 18:05:35 | io.modellerpir: html/io/modellerpir.html |
| 28-Nov-2025 18:05:35 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 28-Nov-2025 18:05:35 | pdbmcviewer: html/features/pdbviewer.html |
| 28-Nov-2025 18:05:35 | groovy.colours: html/features/groovy.html#groovyColours |
| 28-Nov-2025 18:05:35 | seqmappings: html/features/seqmappings.html |
| 28-Nov-2025 18:05:35 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 28-Nov-2025 18:05:35 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 28-Nov-2025 18:05:35 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 28-Nov-2025 18:05:35 | search: html/features/search.html |
| 28-Nov-2025 18:05:35 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 28-Nov-2025 18:05:35 | alformats: html/io/fileformats.html |
| 28-Nov-2025 18:05:35 | strucprefs: html/features/preferences.html#structure |
| 28-Nov-2025 18:05:35 | siftsmapping: html/features/siftsmapping.html |
| 28-Nov-2025 18:05:35 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 28-Nov-2025 18:05:35 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 28-Nov-2025 18:05:35 | newkeys: html/features/newkeystrokes.html |
| 28-Nov-2025 18:05:35 | importvcf.attribs: html/features/importvcf.html#attribs |
| 28-Nov-2025 18:05:35 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 28-Nov-2025 18:05:35 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 28-Nov-2025 18:05:35 | jalarchive: html/features/jalarchive.html |
| 28-Nov-2025 18:05:35 | newsreader: html/webServices/newsreader.html |
| 28-Nov-2025 18:05:35 | jalviewcltool: html/features/commandline.html#script |
| 28-Nov-2025 18:05:35 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 28-Nov-2025 18:05:35 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 28-Nov-2025 18:05:35 | paematrixformat: html/io/paematrixformat.html |
| 28-Nov-2025 18:05:35 | overview: html/features/overview.html |
| 28-Nov-2025 18:05:35 | 0 invalid map urls |
| 28-Nov-2025 18:05:35 | 0 invalid image attributes |
| 28-Nov-2025 18:05:35 | 520 internal href links (120 with anchors) |
| 28-Nov-2025 18:05:35 | 0 invalid internal href links |
| 28-Nov-2025 18:05:35 | 0 invalid internal anchor links |
| 28-Nov-2025 18:05:35 | 112 external href links |
| 28-Nov-2025 18:05:35 | External links not verified as internet not available |
| 28-Nov-2025 18:05:35 | *** Success *** |
| 28-Nov-2025 18:05:36 | |
| 28-Nov-2025 18:05:36 | > Task :jar |
| 28-Nov-2025 18:05:37 | > Task :syncJars |
| 28-Nov-2025 18:05:37 | > Task :makeDist |
| 28-Nov-2025 18:05:44 | > Task :shadowJar |
| 28-Nov-2025 18:05:44 | |
| 28-Nov-2025 18:05:44 | > Task :getdownImagesCopy |
| 28-Nov-2025 18:05:44 | Execution optimizations have been disabled for task ':getdownImagesCopy' to ensure correctness due to the following reasons: |
| 28-Nov-2025 18:05:44 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-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. |
| 28-Nov-2025 18:05:44 | |
| 28-Nov-2025 18:05:44 | > Task :getdownImagesProcess |
| 28-Nov-2025 18:05:44 | > Task :getdownImages |
| 28-Nov-2025 18:05:44 | > Task :getdownWebsiteBuild |
| 28-Nov-2025 18:05:46 | 2025/11/28 18:05:44:926 WARNING Starting without install4j classes |
| 28-Nov-2025 18:05:46 | 2025/11/28 18:05:45:827 WARNING Starting without install4j classes |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | > Task :getdownDigest |
| 28-Nov-2025 18:05:46 | Generating digest file './build/website/docroot/getdown/default/1.8/digest.txt'... |
| 28-Nov-2025 18:05:46 | Generating digest file './build/website/docroot/getdown/default/1.8/digest2.txt'... |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | > Task :getdown |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 28-Nov-2025 18:05:46 | Please consult deprecation warnings for more details. |
| 28-Nov-2025 18:05:46 | |
| 28-Nov-2025 18:05:46 | BUILD SUCCESSFUL in 2m 35s |
| 28-Nov-2025 18:05:46 | 21 actionable tasks: 18 executed, 3 up-to-date |
| 28-Nov-2025 18:05:46 | Finished task 'Jalview distribution for Java 8' with result: Success |
| 28-Nov-2025 18:05:46 | Skipping execution of task 'Create JVL files from getdown.txt' as it is disabled |
| 28-Nov-2025 18:05:46 | Running post build plugin 'NCover Results Collector' |
| 28-Nov-2025 18:05:46 | Running post build plugin 'Artifact Copier' |
| 28-Nov-2025 18:05:46 | Publishing an artifact: Jalview executables |
| 28-Nov-2025 18:05:47 | Finished publishing of artifact Shared artifact: [Jalview executables], pattern: [**/*] anchored at: [build/libs] in 201.4 ms |
| 28-Nov-2025 18:05:47 | Publishing an artifact: install4j installers |
| 28-Nov-2025 18:05:47 | Unable to publish artifact [install4j installers]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/install4j does not exist. |
| 28-Nov-2025 18:05:47 | The artifact hasn't been successfully published after 79.92 μs |
| 28-Nov-2025 18:05:47 | Publishing an artifact: getdown-channel |
| 28-Nov-2025 18:05:47 | Unable to publish artifact [getdown-channel]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/getdown/website does not exist. |
| 28-Nov-2025 18:05:47 | The artifact hasn't been successfully published after 27.46 μs |
| 28-Nov-2025 18:05:47 | Publishing an artifact: Jalview getdown launcher |
| 28-Nov-2025 18:05:47 | Unable to publish artifact [Jalview getdown launcher]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/getdown/files does not exist. |
| 28-Nov-2025 18:05:47 | The artifact hasn't been successfully published after 24.28 μs |
| 28-Nov-2025 18:05:47 | Publishing an artifact: getdown build for website |
| 28-Nov-2025 18:05:48 | Finished publishing of artifact Shared artifact: [getdown build for website], pattern: [**/*] anchored at: [build/website/docroot/getdown] in 1.023 s |
| 28-Nov-2025 18:05:48 | Publishing an artifact: getdown build for archive |
| 28-Nov-2025 18:05:48 | Unable to publish artifact [getdown build for archive]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GPC652-JOB1/build/website/docroot/old does not exist. |
| 28-Nov-2025 18:05:48 | The artifact hasn't been successfully published after 60.77 μs |
| 28-Nov-2025 18:05:48 | Running post build plugin 'Artifactory Release Management Staging' |
| 28-Nov-2025 18:05:48 | Running post build plugin 'Artifactory Build Info Copier' |
| 28-Nov-2025 18:05:48 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 28-Nov-2025 18:05:48 | Running post build plugin 'npm Cache Cleanup' |
| 28-Nov-2025 18:05:48 | Running post build plugin 'Clover Results Collector' |
| 28-Nov-2025 18:05:48 | Running post build plugin 'Docker Container Cleanup' |
| 28-Nov-2025 18:05:48 | Finalising the build... |
| 28-Nov-2025 18:05:48 | Stopping timer. |
| 28-Nov-2025 18:05:48 | Build JB-GPC652-JOB1-3 completed. |
| 28-Nov-2025 18:05:48 | Running on server: post build plugin 'NCover Results Collector' |
| 28-Nov-2025 18:05:48 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 28-Nov-2025 18:05:48 | Running on server: post build plugin 'Clover Delta Calculator' |
| 28-Nov-2025 18:05:48 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 28-Nov-2025 18:05:48 | All post build plugins have finished |
| 28-Nov-2025 18:05:48 | Generating build results summary... |
| 28-Nov-2025 18:05:48 | Saving build results to disk... |
| 28-Nov-2025 18:05:48 | Logging substituted variables... |
| 28-Nov-2025 18:05:48 | Indexing build results... |
| 28-Nov-2025 18:05:48 | Finished building JB-GPC652-JOB1-3. |