simple 28-Nov-2025 18:05:48 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GDL109-JOB1-3) started building on agent Default Agent simple 28-Nov-2025 18:05:48 simple 28-Nov-2025 18:05:48 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1 simple 28-Nov-2025 18:05:48 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GDL109-JOB1-3) simple 28-Nov-2025 18:05:48 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 28-Nov-2025 18:05:48 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1 simple 28-Nov-2025 18:05:48 Updating source code to revision: 6f2c311824a96fc172e1713db11e8c1cdb24e48c simple 28-Nov-2025 18:05:49 Fetching 'refs/heads/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 28-Nov-2025 18:05:49 Checking out revision 6f2c311824a96fc172e1713db11e8c1cdb24e48c. simple 28-Nov-2025 18:05:49 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 28-Nov-2025 18:05:49 c0746f1..6f2c311 bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest simple 28-Nov-2025 18:05:49 Already on 'bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' simple 28-Nov-2025 18:05:49 Your branch is behind 'origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' by 3 commits, and can be fast-forwarded. simple 28-Nov-2025 18:05:49 (use "git pull" to update your local branch) simple 28-Nov-2025 18:05:49 HEAD is now at 6f2c311 JAL-4633 attempted workaround - really need a j2stest to verify that the j2s-ed expression is correct. simple 28-Nov-2025 18:05:49 Updated source code to revision: 6f2c311824a96fc172e1713db11e8c1cdb24e48c simple 28-Nov-2025 18:05:49 Finished task 'Checkout Default Repository' with result: Success simple 28-Nov-2025 18:05:49 Running pre-build action: VCS Version Collector simple 28-Nov-2025 18:05:49 Running pre-build action: Artifactory Release Staging command 28-Nov-2025 18:05:49 Substituting variable: ${bamboo.planKey} with JB-GDL109 simple 28-Nov-2025 18:05:49 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 28-Nov-2025 18:05:49 Bamboo Artifactory Plugin version: 2.6.2 command 28-Nov-2025 18:05:49 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GDL109-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL109 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_dependency_parent_0=JB-GDB727-4\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nCATALINA_PID=/home/bamboo/latest/work/bamboo.pid\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL109-JOB1-3\nJAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL109-JOB1\nbamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498588_git_username=\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_buildNumber=3\nPWD=/\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL109-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_shortPlanKey=GDL109\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_buildTimeStamp=2025-11-28T18:00:29.753Z\nbamboo_repository_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_repository_46498588_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildResultKey=JB-GDL109-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nSHLVL=1\nbamboo_repository_46498588_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_CHANNEL=DEVELOP\nbamboo_repository_46498588_name=Jalview Gitlab\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nJAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/\nLANG=en_GB.UTF-8\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498588_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_plan_storageTag=plan-46302747\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_repository_46498588_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498588_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\nbamboo_planKey=JB-GDL109\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 28-Nov-2025 18:05:51 build 28-Nov-2025 18:05:51 > Configure project : build 28-Nov-2025 18:05:51 Using properties from file './utils/channels/default/channel_gradle.properties' build 28-Nov-2025 18:05:51 JALVIEW_VERSION is set to '2.11.5.1' build 28-Nov-2025 18:05:51 HEADLESS BUILD build 28-Nov-2025 18:05:51 J2S ENABLED build 28-Nov-2025 18:05:51 Using a BUILD profile. build 28-Nov-2025 18:05:51 eclipseDir exists build 28-Nov-2025 18:05:51 build 28-Nov-2025 18:05:51 > Task :clean build 28-Nov-2025 18:05:51 > Task :cleanPackageDir build 28-Nov-2025 18:05:51 > Task :getdownImagesCopy build 28-Nov-2025 18:05:51 > Task :getdownImagesProcess build 28-Nov-2025 18:05:51 > Task :getdownImages build 28-Nov-2025 18:05:52 > Task :copyHelp build 28-Nov-2025 18:05:53 > Task :buildIndices build 28-Nov-2025 18:05:53 > Task :copyResources build 28-Nov-2025 18:05:53 > Task :copyChannelResources build 28-Nov-2025 18:05:53 build 28-Nov-2025 18:05:53 > Task :createBuildProperties build 28-Nov-2025 18:05:53 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 28-Nov-2025 18:05:53 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:05:53 build 28-Nov-2025 18:05:53 > Task :buildResources build 28-Nov-2025 18:05:53 > Task :copyDocs build 28-Nov-2025 18:05:53 build 28-Nov-2025 18:05:53 > Task :convertMdFiles build 28-Nov-2025 18:05:53 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 28-Nov-2025 18:05:53 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build/doc/releaseprocess.html build 28-Nov-2025 18:05:53 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 28-Nov-2025 18:05:53 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build/doc/building.html build 28-Nov-2025 18:05:53 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build/doc/jalview-projects.html build 28-Nov-2025 18:05:54 build 28-Nov-2025 18:05:54 > Task :releasesTemplates build 28-Nov-2025 18:05:54 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 28-Nov-2025 18:05:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:05:54 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:05:54 Stripping rc/test/etc for 2_11_5_1 build 28-Nov-2025 18:05:54 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md build 28-Nov-2025 18:05:54 build 28-Nov-2025 18:05:54 > Task :prepare build 28-Nov-2025 18:05:56 build 28-Nov-2025 18:05:56 > Task :compileJava build 28-Nov-2025 18:05:56 Setting target compatibility to 11 error 28-Nov-2025 18:06:03 Note: Some input files use or override a deprecated API. error 28-Nov-2025 18:06:03 Note: Recompile with -Xlint:deprecation for details. error 28-Nov-2025 18:06:03 Note: Some input files use unchecked or unsafe operations. error 28-Nov-2025 18:06:03 Note: Recompile with -Xlint:unchecked for details. build 28-Nov-2025 18:06:04 build 28-Nov-2025 18:06:04 > Task :processResources build 28-Nov-2025 18:06:04 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-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. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:04 build 28-Nov-2025 18:06:04 > Task :classes build 28-Nov-2025 18:06:05 build 28-Nov-2025 18:06:05 > Task :compileLinkCheck build 28-Nov-2025 18:06:05 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 28-Nov-2025 18:06:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:05 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. build 28-Nov-2025 18:06:07 build 28-Nov-2025 18:06:07 > Task :linkCheck build 28-Nov-2025 18:06:07 Checking help file links build 28-Nov-2025 18:08:14 build 28-Nov-2025 18:08:14 Results: build 28-Nov-2025 18:08:14 161 distinct help targets build 28-Nov-2025 18:08:14 161 help mappings build 28-Nov-2025 18:08:14 0 invalid targets build 28-Nov-2025 18:08:14 31 unused targets build 28-Nov-2025 18:08:14 uniprotfetcher: html/features/uniprotsequencefetcher.html build 28-Nov-2025 18:08:14 overviewprefs: html/features/preferences.html#overview build 28-Nov-2025 18:08:14 cdnafeatures: html/features/codingfeatures.html build 28-Nov-2025 18:08:14 startupprefs: html/features/preferences.html#startup build 28-Nov-2025 18:08:14 ensemblfetch: html/features/ensemblsequencefetcher.html build 28-Nov-2025 18:08:14 io.modellerpir: html/io/modellerpir.html build 28-Nov-2025 18:08:14 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 28-Nov-2025 18:08:14 pdbmcviewer: html/features/pdbviewer.html build 28-Nov-2025 18:08:14 groovy.colours: html/features/groovy.html#groovyColours build 28-Nov-2025 18:08:14 seqmappings: html/features/seqmappings.html build 28-Nov-2025 18:08:14 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 28-Nov-2025 18:08:14 splitframe.mirrorfonts: html/features/splitView.html#mirror build 28-Nov-2025 18:08:14 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 28-Nov-2025 18:08:14 search: html/features/search.html build 28-Nov-2025 18:08:14 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 28-Nov-2025 18:08:14 alformats: html/io/fileformats.html build 28-Nov-2025 18:08:14 strucprefs: html/features/preferences.html#structure build 28-Nov-2025 18:08:14 siftsmapping: html/features/siftsmapping.html build 28-Nov-2025 18:08:14 chimera.annotxfer: html/features/chimera.html#annotxfer build 28-Nov-2025 18:08:14 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 28-Nov-2025 18:08:14 newkeys: html/features/newkeystrokes.html build 28-Nov-2025 18:08:14 importvcf.attribs: html/features/importvcf.html#attribs build 28-Nov-2025 18:08:14 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 28-Nov-2025 18:08:14 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 28-Nov-2025 18:08:14 jalarchive: html/features/jalarchive.html build 28-Nov-2025 18:08:14 newsreader: html/webServices/newsreader.html build 28-Nov-2025 18:08:14 jalviewcltool: html/features/commandline.html#script build 28-Nov-2025 18:08:14 popMenuAddref: html/menus/popupMenu.html#addrefannot build 28-Nov-2025 18:08:14 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 28-Nov-2025 18:08:14 paematrixformat: html/io/paematrixformat.html build 28-Nov-2025 18:08:14 overview: html/features/overview.html build 28-Nov-2025 18:08:14 0 invalid map urls build 28-Nov-2025 18:08:14 0 invalid image attributes build 28-Nov-2025 18:08:14 520 internal href links (120 with anchors) build 28-Nov-2025 18:08:14 0 invalid internal href links build 28-Nov-2025 18:08:14 0 invalid internal anchor links build 28-Nov-2025 18:08:14 112 external href links build 28-Nov-2025 18:08:14 External links not verified as internet not available build 28-Nov-2025 18:08:14 *** Success *** build 28-Nov-2025 18:08:14 build 28-Nov-2025 18:08:14 > Task :jar build 28-Nov-2025 18:08:14 > Task :syncJars build 28-Nov-2025 18:08:14 > Task :makeDist build 28-Nov-2025 18:08:14 > Task :getdownWebsiteBuild error 28-Nov-2025 18:08:16 2025/11/28 18:08:15:307 WARNING Starting without install4j classes error 28-Nov-2025 18:08:16 2025/11/28 18:08:15:988 WARNING Starting without install4j classes build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 > Task :getdownDigest build 28-Nov-2025 18:08:16 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 28-Nov-2025 18:08:16 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 > Task :getdown build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 28-Nov-2025 18:08:16 Please consult deprecation warnings for more details. build 28-Nov-2025 18:08:16 build 28-Nov-2025 18:08:16 BUILD SUCCESSFUL in 2m 26s build 28-Nov-2025 18:08:16 21 actionable tasks: 21 executed simple 28-Nov-2025 18:08:17 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 28-Nov-2025 18:08:17 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 28-Nov-2025 18:08:17 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job #3 (JB-GDL109-JOB1-3)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL109-JOB1-3-ScriptBuildTask-3898188727355261111.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_dependency_parent_0=JB-GDB727-4\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL109-JOB1-3\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL109-JOB1\nbamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_repository_46498588_git_username=\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_buildNumber=3\nbamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse\nbamboo_shortJobName=Default Job\nbamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL109-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_shortPlanKey=GDL109\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_buildTimeStamp=2025-11-28T18:00:29.753Z\nbamboo_repository_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_repository_46498588_previous_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff\nbamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildResultKey=JB-GDL109-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_repository_46498588_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_CHANNEL=DEVELOP\nbamboo_repository_46498588_name=Jalview Gitlab\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_name=Jalview Gitlab\nbamboo_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-GDL109 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498588_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\nbamboo_plan_storageTag=plan-46302747\nbamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle\nbamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache\nbamboo_repository_46498588_revision_number=6f2c311824a96fc172e1713db11e8c1cdb24e48c\nbamboo_planRepository_1_username=\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498588_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_capability_system_builder_ant_Ant=/usr/share/ant\nbamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven\nbamboo_tmp_directory=/srv/bamboo/bamboo-home/temp\nbamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL109-JOB1\nbamboo_planKey=JB-GDL109\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest\n simple 28-Nov-2025 18:08:17 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 28-Nov-2025 18:08:17 Running post build plugin 'NCover Results Collector' simple 28-Nov-2025 18:08:17 Running post build plugin 'Artifact Copier' simple 28-Nov-2025 18:08:17 Publishing an artifact: getdown simple 28-Nov-2025 18:08:17 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 118.7 ms simple 28-Nov-2025 18:08:17 Running post build plugin 'Artifactory Release Management Staging' simple 28-Nov-2025 18:08:17 Running post build plugin 'Artifactory Build Info Copier' simple 28-Nov-2025 18:08:17 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 28-Nov-2025 18:08:17 Running post build plugin 'npm Cache Cleanup' simple 28-Nov-2025 18:08:17 Running post build plugin 'Clover Results Collector' simple 28-Nov-2025 18:08:17 Running post build plugin 'Docker Container Cleanup' simple 28-Nov-2025 18:08:17 Finalising the build... simple 28-Nov-2025 18:08:17 Stopping timer. simple 28-Nov-2025 18:08:17 Build JB-GDL109-JOB1-3 completed. simple 28-Nov-2025 18:08:17 Running on server: post build plugin 'NCover Results Collector' simple 28-Nov-2025 18:08:17 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 28-Nov-2025 18:08:17 Running on server: post build plugin 'Clover Delta Calculator' simple 28-Nov-2025 18:08:17 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 28-Nov-2025 18:08:17 All post build plugins have finished simple 28-Nov-2025 18:08:17 Generating build results summary... simple 28-Nov-2025 18:08:17 Saving build results to disk... simple 28-Nov-2025 18:08:17 Logging substituted variables... simple 28-Nov-2025 18:08:17 Indexing build results... simple 28-Nov-2025 18:08:17 Finished building JB-GDL109-JOB1-3.