simple 16-Sep-2024 16:14:26 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job #3 (JB-GDL19-JOB1-3) started building on agent Default Agent simple 16-Sep-2024 16:14:26 simple 16-Sep-2024 16:14:26 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1 simple 16-Sep-2024 16:14:26 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job #3 (JB-GDL19-JOB1-3) simple 16-Sep-2024 16:14:26 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 16-Sep-2024 16:14:26 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1 simple 16-Sep-2024 16:14:26 Updating source code to revision: 13190d3a1ce589bfb7bd24e81e2c8660a88ff161 simple 16-Sep-2024 16:14:26 Fetching 'refs/heads/bug/JAL-4427_HTML_code_in_sequence_ID_text' from 'http://source.jalview.org/git/jalview.git'. simple 16-Sep-2024 16:14:27 Checking out revision 13190d3a1ce589bfb7bd24e81e2c8660a88ff161. simple 16-Sep-2024 16:14:29 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 simple 16-Sep-2024 16:14:29 47cde5d..13190d3 bug/JAL-4427_HTML_code_in_sequence_ID_text -> origin/bug/JAL-4427_HTML_code_in_sequence_ID_text simple 16-Sep-2024 16:14:29 8e8ae2a..41e8b79 develop -> origin/develop simple 16-Sep-2024 16:14:29 5f218a6..03ba07a feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_update -> origin/feature/JAL-4386_JAL-4435_trees_from_annotations_on_alignment_2114_update simple 16-Sep-2024 16:14:29 a16e52e..e6d7db1 feature/JAL-4386_calculate_tree_using_secondary_structure_annotation -> origin/feature/JAL-4386_calculate_tree_using_secondary_structure_annotation simple 16-Sep-2024 16:14:29 cea846e..82ffdea improvement/JAL-4461_select_format_from_extension -> origin/improvement/JAL-4461_select_format_from_extension simple 16-Sep-2024 16:14:29 5198f96..adb9d64 releases/Release_2_11_4_Branch -> origin/releases/Release_2_11_4_Branch simple 16-Sep-2024 16:14:29 Already on 'bug/JAL-4427_HTML_code_in_sequence_ID_text' simple 16-Sep-2024 16:14:29 Your branch is behind 'origin/bug/JAL-4427_HTML_code_in_sequence_ID_text' by 1 commit, and can be fast-forwarded. simple 16-Sep-2024 16:14:29 (use "git pull" to update your local branch) simple 16-Sep-2024 16:14:29 HEAD is now at 13190d3 JAL-4427 Added test cases and a minor correction simple 16-Sep-2024 16:14:29 Updated source code to revision: 13190d3a1ce589bfb7bd24e81e2c8660a88ff161 simple 16-Sep-2024 16:14:29 Finished task 'Checkout Default Repository' with result: Success simple 16-Sep-2024 16:14:29 Running pre-build action: VCS Version Collector simple 16-Sep-2024 16:14:29 Running pre-build action: Artifactory Release Staging command 16-Sep-2024 16:14:29 Substituting variable: ${bamboo.planKey} with JB-GDL19 simple 16-Sep-2024 16:14:29 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 16-Sep-2024 16:14:29 Bamboo Artifactory Plugin version: 2.6.2 command 16-Sep-2024 16:14:29 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job #3 (JB-GDL19-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL19 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_dependency_parent_0=JB-GDB615-3\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-4427_HTML_code_in_sequence_ID_text\nbamboo_repository_revision_number=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL19-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-GDL19-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL19-JOB1\nbamboo_shortPlanName=bug-JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_46498053_git_username=\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-GDL19-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nSHELL=/bin/bash\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_shortPlanKey=GDL19\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_buildTimeStamp=2024-09-16T16:14:26.901+01:00\nbamboo_repository_previous_revision_number=47cde5d652a565b540c345825c638fc4c167c4d7\nbamboo_repository_git_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_buildResultKey=JB-GDL19-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498053_previous_revision_number=47cde5d652a565b540c345825c638fc4c167c4d7\nbamboo_repository_name=Jalview Git\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_repository_46498053_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498053_name=Jalview Git\nbamboo_planRepository_branchDisplayName=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4427_HTML_code_in_sequence_ID_text\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_46498053_revision_number=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_plan_storageTag=plan-46301705\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_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=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498053_git_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_repository_46498053_branch_name=bug/JAL-4427_HTML_code_in_sequence_ID_text\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-GDL19-JOB1\nbamboo_planKey=JB-GDL19\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4427_HTML_code_in_sequence_ID_text\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 16-Sep-2024 16:14:31 build 16-Sep-2024 16:14:31 > Configure project : build 16-Sep-2024 16:14:31 Using properties from file './utils/channels/default/channel_gradle.properties' build 16-Sep-2024 16:14:31 JALVIEW_VERSION is set to '2.11.4.0' build 16-Sep-2024 16:14:31 HEADLESS BUILD build 16-Sep-2024 16:14:31 J2S ENABLED build 16-Sep-2024 16:14:31 Using a BUILD profile. build 16-Sep-2024 16:14:31 eclipseDir exists build 16-Sep-2024 16:14:31 build 16-Sep-2024 16:14:31 > Task :clean build 16-Sep-2024 16:14:31 > Task :cleanPackageDir build 16-Sep-2024 16:14:31 > Task :getdownImagesCopy build 16-Sep-2024 16:14:31 > Task :getdownImagesProcess build 16-Sep-2024 16:14:31 > Task :getdownImages build 16-Sep-2024 16:14:32 > Task :copyHelp build 16-Sep-2024 16:14:35 > Task :buildIndices build 16-Sep-2024 16:14:35 > Task :copyResources build 16-Sep-2024 16:14:35 > Task :copyChannelResources build 16-Sep-2024 16:14:35 build 16-Sep-2024 16:14:35 > Task :createBuildProperties build 16-Sep-2024 16:14:35 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 16-Sep-2024 16:14:35 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:35 build 16-Sep-2024 16:14:35 > Task :buildResources build 16-Sep-2024 16:14:35 > Task :copyDocs build 16-Sep-2024 16:14:35 build 16-Sep-2024 16:14:35 > Task :convertMdFiles build 16-Sep-2024 16:14:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 16-Sep-2024 16:14:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/build/resources/doc_build/doc/releaseprocess.html build 16-Sep-2024 16:14:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 16-Sep-2024 16:14:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/build/resources/doc_build/doc/building.html build 16-Sep-2024 16:14:35 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/build/resources/doc_build/doc/jalview-projects.html build 16-Sep-2024 16:14:36 build 16-Sep-2024 16:14:36 > Task :releasesTemplates build 16-Sep-2024 16:14:36 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 16-Sep-2024 16:14:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:36 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:36 Stripping rc/test/etc for 2_11_4_0 build 16-Sep-2024 16:14:36 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_0.md build 16-Sep-2024 16:14:36 build 16-Sep-2024 16:14:36 > Task :prepare build 16-Sep-2024 16:14:38 build 16-Sep-2024 16:14:38 > Task :compileJava build 16-Sep-2024 16:14:38 Setting target compatibility to 11 error 16-Sep-2024 16:14:45 Note: Some input files use or override a deprecated API. error 16-Sep-2024 16:14:45 Note: Recompile with -Xlint:deprecation for details. error 16-Sep-2024 16:14:45 Note: Some input files use unchecked or unsafe operations. error 16-Sep-2024 16:14:45 Note: Recompile with -Xlint:unchecked for details. build 16-Sep-2024 16:14:46 build 16-Sep-2024 16:14:46 > Task :processResources build 16-Sep-2024 16:14:46 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:46 build 16-Sep-2024 16:14:46 > Task :classes build 16-Sep-2024 16:14:47 build 16-Sep-2024 16:14:47 > Task :compileLinkCheck build 16-Sep-2024 16:14:47 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 16-Sep-2024 16:14:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:47 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-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 16-Sep-2024 16:14:49 build 16-Sep-2024 16:14:49 > Task :linkCheck build 16-Sep-2024 16:14:49 Checking help file links build 16-Sep-2024 16:16:55 build 16-Sep-2024 16:16:55 Results: build 16-Sep-2024 16:16:55 159 distinct help targets build 16-Sep-2024 16:16:55 159 help mappings build 16-Sep-2024 16:16:55 0 invalid targets build 16-Sep-2024 16:16:55 32 unused targets build 16-Sep-2024 16:16:55 uniprotfetcher: html/features/uniprotsequencefetcher.html build 16-Sep-2024 16:16:55 overviewprefs: html/features/preferences.html#overview build 16-Sep-2024 16:16:55 cdnafeatures: html/features/codingfeatures.html build 16-Sep-2024 16:16:55 startupprefs: html/features/preferences.html#startup build 16-Sep-2024 16:16:55 ensemblfetch: html/features/ensemblsequencefetcher.html build 16-Sep-2024 16:16:55 io.modellerpir: html/io/modellerpir.html build 16-Sep-2024 16:16:55 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 16-Sep-2024 16:16:55 pdbmcviewer: html/features/pdbviewer.html build 16-Sep-2024 16:16:55 workingwithpae: html/features/paematrices.html build 16-Sep-2024 16:16:55 groovy.colours: html/features/groovy.html#groovyColours build 16-Sep-2024 16:16:55 seqmappings: html/features/seqmappings.html build 16-Sep-2024 16:16:55 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 16-Sep-2024 16:16:55 splitframe.mirrorfonts: html/features/splitView.html#mirror build 16-Sep-2024 16:16:55 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 16-Sep-2024 16:16:55 search: html/features/search.html build 16-Sep-2024 16:16:55 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 16-Sep-2024 16:16:55 alformats: html/io/fileformats.html build 16-Sep-2024 16:16:55 strucprefs: html/features/preferences.html#structure build 16-Sep-2024 16:16:55 siftsmapping: html/features/siftsmapping.html build 16-Sep-2024 16:16:55 chimera.annotxfer: html/features/chimera.html#annotxfer build 16-Sep-2024 16:16:55 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 16-Sep-2024 16:16:55 newkeys: html/features/newkeystrokes.html build 16-Sep-2024 16:16:55 importvcf.attribs: html/features/importvcf.html#attribs build 16-Sep-2024 16:16:55 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 16-Sep-2024 16:16:55 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 16-Sep-2024 16:16:55 jalarchive: html/features/jalarchive.html build 16-Sep-2024 16:16:55 newsreader: html/webServices/newsreader.html build 16-Sep-2024 16:16:55 jalviewcltool: html/features/commandline.html#script build 16-Sep-2024 16:16:55 popMenuAddref: html/menus/popupMenu.html#addrefannot build 16-Sep-2024 16:16:55 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 16-Sep-2024 16:16:55 paematrixformat: html/io/paematrixformat.html build 16-Sep-2024 16:16:55 overview: html/features/overview.html build 16-Sep-2024 16:16:55 0 invalid map urls build 16-Sep-2024 16:16:55 0 invalid image attributes build 16-Sep-2024 16:16:55 500 internal href links (107 with anchors) build 16-Sep-2024 16:16:55 0 invalid internal href links build 16-Sep-2024 16:16:55 0 invalid internal anchor links build 16-Sep-2024 16:16:55 113 external href links build 16-Sep-2024 16:16:55 External links not verified as internet not available build 16-Sep-2024 16:16:55 *** Success *** build 16-Sep-2024 16:16:55 build 16-Sep-2024 16:16:55 > Task :jar build 16-Sep-2024 16:16:56 > Task :syncJars build 16-Sep-2024 16:16:56 > Task :makeDist build 16-Sep-2024 16:16:57 > Task :getdownWebsiteBuild build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 > Task :getdownDigest build 16-Sep-2024 16:16:58 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 16-Sep-2024 16:16:58 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 > Task :getdown build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 16-Sep-2024 16:16:58 Please consult deprecation warnings for more details. build 16-Sep-2024 16:16:58 build 16-Sep-2024 16:16:58 BUILD SUCCESSFUL in 2m 29s build 16-Sep-2024 16:16:58 21 actionable tasks: 21 executed error 16-Sep-2024 16:16:58 2024/09/16 16:16:57:596 WARNING Starting without install4j classes error 16-Sep-2024 16:16:58 2024/09/16 16:16:58:202 WARNING Starting without install4j classes simple 16-Sep-2024 16:16:59 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 16-Sep-2024 16:16:59 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 16-Sep-2024 16:16:59 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job #3 (JB-GDL19-JOB1-3)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL19-JOB1-3-ScriptBuildTask-363066184302151928.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_dependency_parent_0=JB-GDB615-3\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_repository_revision_number=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL19-JOB1-3\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL19-JOB1\nbamboo_planRepository_1_name=Jalview Git\nbamboo_buildKey=JB-GDL19-JOB1\nbamboo_shortPlanName=bug-JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_planRepository_name=Jalview Git\nbamboo_repository_46498053_git_username=\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-GDL19-JOB1-3\nbamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_shortPlanKey=GDL19\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_buildTimeStamp=2024-09-16T16:14:26.901+01:00\nbamboo_repository_previous_revision_number=47cde5d652a565b540c345825c638fc4c167c4d7\nbamboo_repository_git_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_buildResultKey=JB-GDL19-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4427_HTML_code_in_sequence_ID_text - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498053_previous_revision_number=47cde5d652a565b540c345825c638fc4c167c4d7\nbamboo_repository_name=Jalview Git\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-GDL19 -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_repository_46498053_git_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609\nbamboo_capability_system_git_executable=/bin/git\nbamboo_repository_git_username=\nbamboo_repository_46498053_name=Jalview Git\nbamboo_planRepository_branchDisplayName=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_repository_46498053_revision_number=13190d3a1ce589bfb7bd24e81e2c8660a88ff161\nbamboo_plan_storageTag=plan-46301705\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_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=http://source.jalview.org/git/jalview.git\nbamboo_repository_46498053_git_branch=bug/JAL-4427_HTML_code_in_sequence_ID_text\nbamboo_repository_46498053_branch_name=bug/JAL-4427_HTML_code_in_sequence_ID_text\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-GDL19-JOB1\nbamboo_planKey=JB-GDL19\nbamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4427_HTML_code_in_sequence_ID_text\n simple 16-Sep-2024 16:16:59 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 16-Sep-2024 16:16:59 Running post build plugin 'NCover Results Collector' simple 16-Sep-2024 16:16:59 Running post build plugin 'Artifact Copier' simple 16-Sep-2024 16:16:59 Publishing an artifact: getdown simple 16-Sep-2024 16:16:59 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 93.20 ms simple 16-Sep-2024 16:16:59 Running post build plugin 'Artifactory Release Management Staging' simple 16-Sep-2024 16:16:59 Running post build plugin 'Artifactory Build Info Copier' simple 16-Sep-2024 16:16:59 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 16-Sep-2024 16:16:59 Running post build plugin 'npm Cache Cleanup' simple 16-Sep-2024 16:16:59 Running post build plugin 'Clover Results Collector' simple 16-Sep-2024 16:16:59 Running post build plugin 'Docker Container Cleanup' simple 16-Sep-2024 16:16:59 Finalising the build... simple 16-Sep-2024 16:16:59 Stopping timer. simple 16-Sep-2024 16:16:59 Build JB-GDL19-JOB1-3 completed. simple 16-Sep-2024 16:16:59 Running on server: post build plugin 'NCover Results Collector' simple 16-Sep-2024 16:16:59 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 16-Sep-2024 16:16:59 Running on server: post build plugin 'Clover Delta Calculator' simple 16-Sep-2024 16:16:59 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 16-Sep-2024 16:16:59 All post build plugins have finished simple 16-Sep-2024 16:16:59 Generating build results summary... simple 16-Sep-2024 16:16:59 Saving build results to disk... simple 16-Sep-2024 16:16:59 Logging substituted variables... simple 16-Sep-2024 16:16:59 Indexing build results... simple 16-Sep-2024 16:16:59 Finished building JB-GDL19-JOB1-3.