simple 19-Nov-2025 15:12:16 Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job #3 (JB-GDL104-JOB1-3) started building on agent Default Agent simple 19-Nov-2025 15:12:16 simple 19-Nov-2025 15:12:16 Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1 simple 19-Nov-2025 15:12:16 Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job #3 (JB-GDL104-JOB1-3) simple 19-Nov-2025 15:12:16 Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' simple 19-Nov-2025 15:12:16 Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1 simple 19-Nov-2025 15:12:16 Updating source code to revision: 5579c7411432a1b978a885bb1addf5853f0f3fd4 simple 19-Nov-2025 15:12:16 Fetching 'refs/heads/bug/JAL-4603_export_svg_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'. simple 19-Nov-2025 15:12:17 Checking out revision 5579c7411432a1b978a885bb1addf5853f0f3fd4. simple 19-Nov-2025 15:12:17 From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 simple 19-Nov-2025 15:12:17 cc04385..5579c74 bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence simple 19-Nov-2025 15:12:17 * [new branch] bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest simple 19-Nov-2025 15:12:17 01b48f0..0d10b35 bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection -> origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection simple 19-Nov-2025 15:12:17 * [new branch] bug/JAL-4606_Jmol_incorrect_path_on_windows -> origin/bug/JAL-4606_Jmol_incorrect_path_on_windows simple 19-Nov-2025 15:12:17 2c0064b..b0fd08a development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch simple 19-Nov-2025 15:12:17 * [new branch] feature/JAL-4602_Hide_All_SS_consensus_for_single_provider -> origin/feature/JAL-4602_Hide_All_SS_consensus_for_single_provider simple 19-Nov-2025 15:12:17 * [new branch] patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker simple 19-Nov-2025 15:12:17 * [new branch] test/JAL-4603_test_for_JAL-4603_in_progress -> origin/test/JAL-4603_test_for_JAL-4603_in_progress simple 19-Nov-2025 15:12:17 Already on 'bug/JAL-4603_export_svg_files_missing_part_of_sequence' simple 19-Nov-2025 15:12:17 Your branch is behind 'origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence' by 5 commits, and can be fast-forwarded. simple 19-Nov-2025 15:12:17 (use "git pull" to update your local branch) simple 19-Nov-2025 15:12:17 HEAD is now at 5579c74 JAL-4603 Removed the not-working-test for release patch simple 19-Nov-2025 15:12:17 Updated source code to revision: 5579c7411432a1b978a885bb1addf5853f0f3fd4 simple 19-Nov-2025 15:12:17 Finished task 'Checkout Default Repository' with result: Success simple 19-Nov-2025 15:12:17 Running pre-build action: VCS Version Collector simple 19-Nov-2025 15:12:17 Running pre-build action: Artifactory Release Staging command 19-Nov-2025 15:12:17 Substituting variable: ${bamboo.planKey} with JB-GDL104 simple 19-Nov-2025 15:12:17 Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' simple 19-Nov-2025 15:12:17 Bamboo Artifactory Plugin version: 2.6.2 command 19-Nov-2025 15:12:17 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job #3 (JB-GDL104-JOB1-3)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL104 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB722-7\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-4603_export_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL104-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-GDL104-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL104-JOB1\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_46498557_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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-GDL104-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nSHELL=/bin/bash\nbamboo_repository_46498557_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL104\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_buildTimeStamp=2025-11-19T14:59:55.566Z\nbamboo_repository_previous_revision_number=cc043854810f31ff56d5ceaba4946ff998134151\nbamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL104-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5579c7411432a1b978a885bb1addf5853f0f3fd4\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\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_repository_46498557_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\n_=/usr/bin/java\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498557_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302685\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_repository_46498557_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_type=gitv2\nUSER=bamboo\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_46498557_previous_revision_number=cc043854810f31ff56d5ceaba4946ff998134151\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498557_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-GDL104-JOB1\nbamboo_planKey=JB-GDL104\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nPATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin\n build 19-Nov-2025 15:12:20 build 19-Nov-2025 15:12:20 > Configure project : build 19-Nov-2025 15:12:20 Using properties from file './utils/channels/default/channel_gradle.properties' build 19-Nov-2025 15:12:20 JALVIEW_VERSION is set to '2.11.5.0' build 19-Nov-2025 15:12:20 HEADLESS BUILD build 19-Nov-2025 15:12:20 J2S ENABLED build 19-Nov-2025 15:12:20 Using a BUILD profile. build 19-Nov-2025 15:12:20 eclipseDir exists build 19-Nov-2025 15:12:20 build 19-Nov-2025 15:12:20 > Task :clean build 19-Nov-2025 15:12:20 > Task :cleanPackageDir build 19-Nov-2025 15:12:20 > Task :getdownImagesCopy build 19-Nov-2025 15:12:20 > Task :getdownImagesProcess build 19-Nov-2025 15:12:20 > Task :getdownImages build 19-Nov-2025 15:12:21 > Task :copyHelp build 19-Nov-2025 15:12:22 > Task :buildIndices build 19-Nov-2025 15:12:22 > Task :copyResources build 19-Nov-2025 15:12:22 > Task :copyChannelResources build 19-Nov-2025 15:12:23 build 19-Nov-2025 15:12:23 > Task :createBuildProperties build 19-Nov-2025 15:12:23 Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: build 19-Nov-2025 15:12:23 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:23 build 19-Nov-2025 15:12:23 > Task :buildResources build 19-Nov-2025 15:12:23 > Task :copyDocs build 19-Nov-2025 15:12:23 build 19-Nov-2025 15:12:23 > Task :convertMdFiles build 19-Nov-2025 15:12:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/build/resources/doc_build/doc/README-DMG_creation.html build 19-Nov-2025 15:12:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/build/resources/doc_build/doc/releaseprocess.html build 19-Nov-2025 15:12:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html build 19-Nov-2025 15:12:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/build/resources/doc_build/doc/building.html build 19-Nov-2025 15:12:24 Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/build/resources/doc_build/doc/jalview-projects.html build 19-Nov-2025 15:12:24 build 19-Nov-2025 15:12:24 > Task :releasesTemplates build 19-Nov-2025 15:12:24 Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: build 19-Nov-2025 15:12:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:24 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:24 Stripping rc/test/etc for 2_11_5_0 build 19-Nov-2025 15:12:24 Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_0.md build 19-Nov-2025 15:12:24 build 19-Nov-2025 15:12:24 > Task :prepare build 19-Nov-2025 15:12:26 build 19-Nov-2025 15:12:26 > Task :compileJava build 19-Nov-2025 15:12:26 Setting target compatibility to 11 error 19-Nov-2025 15:12:32 Note: Some input files use or override a deprecated API. error 19-Nov-2025 15:12:32 Note: Recompile with -Xlint:deprecation for details. error 19-Nov-2025 15:12:32 Note: Some input files use unchecked or unsafe operations. error 19-Nov-2025 15:12:32 Note: Recompile with -Xlint:unchecked for details. build 19-Nov-2025 15:12:32 build 19-Nov-2025 15:12:32 > Task :processResources build 19-Nov-2025 15:12:32 Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: build 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:32 build 19-Nov-2025 15:12:32 > Task :classes build 19-Nov-2025 15:12:34 build 19-Nov-2025 15:12:34 > Task :compileLinkCheck build 19-Nov-2025 15:12:34 Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: build 19-Nov-2025 15:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:34 - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-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 19-Nov-2025 15:12:36 build 19-Nov-2025 15:12:36 > Task :linkCheck build 19-Nov-2025 15:12:36 Checking help file links build 19-Nov-2025 15:14:42 build 19-Nov-2025 15:14:42 Results: build 19-Nov-2025 15:14:42 161 distinct help targets build 19-Nov-2025 15:14:42 161 help mappings build 19-Nov-2025 15:14:42 0 invalid targets build 19-Nov-2025 15:14:42 31 unused targets build 19-Nov-2025 15:14:42 uniprotfetcher: html/features/uniprotsequencefetcher.html build 19-Nov-2025 15:14:42 overviewprefs: html/features/preferences.html#overview build 19-Nov-2025 15:14:42 cdnafeatures: html/features/codingfeatures.html build 19-Nov-2025 15:14:42 startupprefs: html/features/preferences.html#startup build 19-Nov-2025 15:14:42 ensemblfetch: html/features/ensemblsequencefetcher.html build 19-Nov-2025 15:14:42 io.modellerpir: html/io/modellerpir.html build 19-Nov-2025 15:14:42 structureandpaefromfile: html/features/structurechooser.html#loadfromfile build 19-Nov-2025 15:14:42 pdbmcviewer: html/features/pdbviewer.html build 19-Nov-2025 15:14:42 groovy.colours: html/features/groovy.html#groovyColours build 19-Nov-2025 15:14:42 seqmappings: html/features/seqmappings.html build 19-Nov-2025 15:14:42 uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts build 19-Nov-2025 15:14:42 splitframe.mirrorfonts: html/features/splitView.html#mirror build 19-Nov-2025 15:14:42 subtMatrices.pam250: html/calculations/scorematrices.html#pam250 build 19-Nov-2025 15:14:42 search: html/features/search.html build 19-Nov-2025 15:14:42 viewingpdbs.reps: html/features/viewingpdbs.html#viewreps build 19-Nov-2025 15:14:42 alformats: html/io/fileformats.html build 19-Nov-2025 15:14:42 strucprefs: html/features/preferences.html#structure build 19-Nov-2025 15:14:42 siftsmapping: html/features/siftsmapping.html build 19-Nov-2025 15:14:42 chimera.annotxfer: html/features/chimera.html#annotxfer build 19-Nov-2025 15:14:42 pdbfts: html/features/pdbsequencefetcher.html#pdbfts build 19-Nov-2025 15:14:42 newkeys: html/features/newkeystrokes.html build 19-Nov-2025 15:14:42 importvcf.attribs: html/features/importvcf.html#attribs build 19-Nov-2025 15:14:42 seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature build 19-Nov-2025 15:14:42 structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch build 19-Nov-2025 15:14:42 jalarchive: html/features/jalarchive.html build 19-Nov-2025 15:14:42 newsreader: html/webServices/newsreader.html build 19-Nov-2025 15:14:42 jalviewcltool: html/features/commandline.html#script build 19-Nov-2025 15:14:42 popMenuAddref: html/menus/popupMenu.html#addrefannot build 19-Nov-2025 15:14:42 splitframe.virtualfeats: html/features/splitView.html#virtualfeats build 19-Nov-2025 15:14:42 paematrixformat: html/io/paematrixformat.html build 19-Nov-2025 15:14:42 overview: html/features/overview.html build 19-Nov-2025 15:14:42 0 invalid map urls build 19-Nov-2025 15:14:42 0 invalid image attributes build 19-Nov-2025 15:14:42 520 internal href links (120 with anchors) build 19-Nov-2025 15:14:42 0 invalid internal href links build 19-Nov-2025 15:14:42 0 invalid internal anchor links build 19-Nov-2025 15:14:42 112 external href links build 19-Nov-2025 15:14:42 External links not verified as internet not available build 19-Nov-2025 15:14:42 *** Success *** build 19-Nov-2025 15:14:43 build 19-Nov-2025 15:14:43 > Task :jar build 19-Nov-2025 15:14:43 > Task :syncJars build 19-Nov-2025 15:14:43 > Task :makeDist build 19-Nov-2025 15:14:44 > Task :getdownWebsiteBuild build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 > Task :getdownDigest build 19-Nov-2025 15:14:46 Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... build 19-Nov-2025 15:14:46 Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 > Task :getdown build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. build 19-Nov-2025 15:14:46 Please consult deprecation warnings for more details. build 19-Nov-2025 15:14:46 build 19-Nov-2025 15:14:46 BUILD SUCCESSFUL in 2m 28s build 19-Nov-2025 15:14:46 21 actionable tasks: 21 executed error 19-Nov-2025 15:14:46 2025/11/19 15:14:44:603 WARNING Starting without install4j classes error 19-Nov-2025 15:14:46 2025/11/19 15:14:45:243 WARNING Starting without install4j classes simple 19-Nov-2025 15:14:46 Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success simple 19-Nov-2025 15:14:46 Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' command 19-Nov-2025 15:14:46 Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job #3 (JB-GDL104-JOB1-3)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL104-JOB1-3-ScriptBuildTask-2619060451706593596.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB722-7\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_repository_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL104-JOB1-3\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL104-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL104-JOB1\nbamboo_shortPlanName=bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_repository_46498557_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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-GDL104-JOB1-3\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498557_revision_number=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL104\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_buildTimeStamp=2025-11-19T14:59:55.566Z\nbamboo_repository_previous_revision_number=cc043854810f31ff56d5ceaba4946ff998134151\nbamboo_repository_git_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL104-JOB1-3\nbamboo_repository_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_export_svg_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=5579c7411432a1b978a885bb1addf5853f0f3fd4\nbamboo_CHANNEL=DEVELOP\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-GDL104 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\nbamboo_buildFailed=false\nbamboo_repository_46498557_name=Jalview Gitlab\nbamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk\nbamboo_planRepository_branch=bug/JAL-4603_export_svg_files_missing_part_of_sequence\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-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_repository_46498557_git_username=\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302685\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_repository_46498557_branch_name=bug/JAL-4603_export_svg_files_missing_part_of_sequence\nbamboo_planRepository_type=gitv2\nbamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache\nbamboo_repository_46498557_previous_revision_number=cc043854810f31ff56d5ceaba4946ff998134151\nbamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498557_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-GDL104-JOB1\nbamboo_planKey=JB-GDL104\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_planRepository_1_branchName=bug/JAL-4603_export_svg_files_missing_part_of_sequence\n simple 19-Nov-2025 15:14:46 Finished task 'Copy JVL file and produce link in HTML' with result: Success simple 19-Nov-2025 15:14:46 Running post build plugin 'NCover Results Collector' simple 19-Nov-2025 15:14:46 Running post build plugin 'Artifact Copier' simple 19-Nov-2025 15:14:46 Publishing an artifact: getdown simple 19-Nov-2025 15:14:46 Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 173.1 ms simple 19-Nov-2025 15:14:46 Running post build plugin 'Artifactory Release Management Staging' simple 19-Nov-2025 15:14:46 Running post build plugin 'Artifactory Build Info Copier' simple 19-Nov-2025 15:14:46 Running post build plugin 'Artifactory Gradle Properties Info Copier' simple 19-Nov-2025 15:14:46 Running post build plugin 'npm Cache Cleanup' simple 19-Nov-2025 15:14:46 Running post build plugin 'Clover Results Collector' simple 19-Nov-2025 15:14:46 Running post build plugin 'Docker Container Cleanup' simple 19-Nov-2025 15:14:46 Finalising the build... simple 19-Nov-2025 15:14:46 Stopping timer. simple 19-Nov-2025 15:14:46 Build JB-GDL104-JOB1-3 completed. simple 19-Nov-2025 15:14:46 Running on server: post build plugin 'NCover Results Collector' simple 19-Nov-2025 15:14:46 Running on server: post build plugin 'Build Hanging Detection Configuration' simple 19-Nov-2025 15:14:46 Running on server: post build plugin 'Clover Delta Calculator' simple 19-Nov-2025 15:14:46 Running on server: post build plugin 'Maven Dependencies Postprocessor' simple 19-Nov-2025 15:14:46 All post build plugins have finished simple 19-Nov-2025 15:14:46 Generating build results summary... simple 19-Nov-2025 15:14:46 Saving build results to disk... simple 19-Nov-2025 15:14:46 Logging substituted variables... simple 19-Nov-2025 15:14:46 Indexing build results... simple 19-Nov-2025 15:14:46 Finished building JB-GDL104-JOB1-3.