simple	03-Dec-2025 16:10:04	Build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #2 (JB-GDL93-JOB1-2) started building on agent Default Agent
simple	03-Dec-2025 16:10:04	
simple	03-Dec-2025 16:10:04	Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1
simple	03-Dec-2025 16:10:04	Executing build Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #2 (JB-GDL93-JOB1-2)
simple	03-Dec-2025 16:10:04	Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout'
simple	03-Dec-2025 16:10:04	Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1
simple	03-Dec-2025 16:10:04	Updating source code to revision: db868848b73d9a08f5ee1b08a269436a41323446
simple	03-Dec-2025 16:10:04	Fetching 'refs/heads/bug/JAL-4603_Export_files_missing_part_of_sequence' from 'https://gitlab.jalview.org/jalview/jalview.git'.
simple	03-Dec-2025 16:10:05	Checking out revision db868848b73d9a08f5ee1b08a269436a41323446.
simple	03-Dec-2025 16:10:05	From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0
simple	03-Dec-2025 16:10:05	   0ef8e14..db86884  bug/JAL-4603_Export_files_missing_part_of_sequence -> origin/bug/JAL-4603_Export_files_missing_part_of_sequence
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4594_ss_consensus_overlap_other_annot -> origin/bug/JAL-4594_ss_consensus_overlap_other_annot
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus -> origin/bug/JAL-4601_manual_import_of_jpred_annotation_data_doesnt_display_ss_consensus
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4603_export_svg_files_missing_part_of_sequence -> origin/bug/JAL-4603_export_svg_files_missing_part_of_sequence
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection -> origin/bug/JAL-4604_new_getdown-launcher_jar_and_buggy_arguments_detection
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4606_Jmol_incorrect_path_on_windows -> origin/bug/JAL-4606_Jmol_incorrect_path_on_windows
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4610_rightColumn_wrappedWidth_fails -> origin/bug/JAL-4610_rightColumn_wrappedWidth_fails
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12 -> origin/bug/JAL-4611_SSConsensus_Not_Shown_in_v2_12
simple	03-Dec-2025 16:10:05	 * [new branch]      bug/JAL-4611_SSConsensus_Preferences -> origin/bug/JAL-4611_SSConsensus_Preferences
simple	03-Dec-2025 16:10:05	   2b57021..e193345  development/JAL-4107_merge_2115_212 -> origin/development/JAL-4107_merge_2115_212
simple	03-Dec-2025 16:10:05	   2c0064b..fae9009  development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch
simple	03-Dec-2025 16:10:05	 * [new branch]      development/Release_2_12_Branch -> origin/development/Release_2_12_Branch
simple	03-Dec-2025 16:10:05	 * [new branch]      feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss -> origin/feature/JAL-4521_Allow_PCA_tree_for_one_seq_mul_ss
simple	03-Dec-2025 16:10:05	 * [new branch]      feature/JAL-4602_Hide_All_SS_consensus_for_single_provider -> origin/feature/JAL-4602_Hide_All_SS_consensus_for_single_provider
simple	03-Dec-2025 16:10:05	 * [new branch]      feature/JAL-835_hhsuite_a3m_support -> origin/feature/JAL-835_hhsuite_a3m_support
simple	03-Dec-2025 16:10:05	 * [new branch]      improvement/JAL-4607_install4j_dark_mode_background_colour -> origin/improvement/JAL-4607_install4j_dark_mode_background_colour
simple	03-Dec-2025 16:10:05	 * [new branch]      improvement/JAL-4620_faster_sim_matrices -> origin/improvement/JAL-4620_faster_sim_matrices
simple	03-Dec-2025 16:10:05	 * [new branch]      patch/JAL-4107_singleThreadTests -> origin/patch/JAL-4107_singleThreadTests
simple	03-Dec-2025 16:10:05	 * [new branch]      patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide
simple	03-Dec-2025 16:10:05	 * [new branch]      patch/JAL-4626_alphafoldVersionTracker -> origin/patch/JAL-4626_alphafoldVersionTracker
simple	03-Dec-2025 16:10:05	   86d2c84..c586364  releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch
simple	03-Dec-2025 16:10:05	 * [new branch]      spike/JAL-4107_wrappedWidthCalcs -> origin/spike/JAL-4107_wrappedWidthCalcs
simple	03-Dec-2025 16:10:05	 * [new branch]      test/JAL-4603_test_for_JAL-4603_in_progress -> origin/test/JAL-4603_test_for_JAL-4603_in_progress
simple	03-Dec-2025 16:10:06	Already on 'bug/JAL-4603_Export_files_missing_part_of_sequence'
simple	03-Dec-2025 16:10:06	Your branch is behind 'origin/bug/JAL-4603_Export_files_missing_part_of_sequence' by 78 commits, and can be fast-forwarded.
simple	03-Dec-2025 16:10:06	  (use "git pull" to update your local branch)
simple	03-Dec-2025 16:10:06	HEAD is now at db86884 JAL-4603 Fixed failed tests in SeqCanvasTest
simple	03-Dec-2025 16:10:06	Updated source code to revision: db868848b73d9a08f5ee1b08a269436a41323446
simple	03-Dec-2025 16:10:06	Finished task 'Checkout Default Repository' with result: Success
simple	03-Dec-2025 16:10:06	Running pre-build action: VCS Version Collector
simple	03-Dec-2025 16:10:06	Running pre-build action: Artifactory Release Staging
command	03-Dec-2025 16:10:06	Substituting variable: ${bamboo.planKey} with JB-GDL93
simple	03-Dec-2025 16:10:06	Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask'
simple	03-Dec-2025 16:10:06	Bamboo Artifactory Plugin version: 2.6.2
command	03-Dec-2025 16:10:06	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #2 (JB-GDL93-JOB1-2)'\n ... running command line: \n/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL93 -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB733-4\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-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL93-JOB1-2\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-GDL93-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL93-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nLOGNAME=bamboo\nbamboo_repository_46498486_previous_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_buildNumber=2\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-GDL93-JOB1-2\nbamboo_repository_46498486_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\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-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL93\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_buildTimeStamp=2025-12-03T16:10:04.058Z\nbamboo_repository_previous_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL93-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=db868848b73d9a08f5ee1b08a269436a41323446\nSHLVL=1\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498486_git_username=\nbamboo_repository_46498486_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\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-4603_Export_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_files_missing_part_of_sequence\nbamboo_repository_46498486_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_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_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302543\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498486_name=Jalview Gitlab\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-GDL93-JOB1\nbamboo_planKey=JB-GDL93\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498486_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nHOME=/home/bamboo\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_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	03-Dec-2025 16:10:08	
build	03-Dec-2025 16:10:08	> Configure project :
build	03-Dec-2025 16:10:08	Using properties from file './utils/channels/default/channel_gradle.properties'
build	03-Dec-2025 16:10:08	JALVIEW_VERSION is set to '2.11.5.1'
build	03-Dec-2025 16:10:08	HEADLESS BUILD
build	03-Dec-2025 16:10:08	J2S ENABLED
build	03-Dec-2025 16:10:08	Using a BUILD profile.
build	03-Dec-2025 16:10:08	eclipseDir exists
build	03-Dec-2025 16:10:09	
build	03-Dec-2025 16:10:09	> Task :clean
build	03-Dec-2025 16:10:09	> Task :cleanPackageDir
build	03-Dec-2025 16:10:09	> Task :getdownImagesCopy
build	03-Dec-2025 16:10:09	> Task :getdownImagesProcess
build	03-Dec-2025 16:10:09	> Task :getdownImages
build	03-Dec-2025 16:10:09	> Task :copyHelp
build	03-Dec-2025 16:10:11	> Task :buildIndices
build	03-Dec-2025 16:10:11	> Task :copyResources
build	03-Dec-2025 16:10:11	> Task :copyChannelResources
build	03-Dec-2025 16:10:11	
build	03-Dec-2025 16:10:11	> Task :createBuildProperties
build	03-Dec-2025 16:10:11	Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons:
build	03-Dec-2025 16:10:11	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:11	
build	03-Dec-2025 16:10:11	> Task :buildResources
build	03-Dec-2025 16:10:11	> Task :copyDocs
build	03-Dec-2025 16:10:11	
build	03-Dec-2025 16:10:11	> Task :convertMdFiles
build	03-Dec-2025 16:10:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/README-DMG_creation.html
build	03-Dec-2025 16:10:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/releaseprocess.html
build	03-Dec-2025 16:10:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html
build	03-Dec-2025 16:10:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/building.html
build	03-Dec-2025 16:10:11	Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/build/resources/doc_build/doc/jalview-projects.html
build	03-Dec-2025 16:10:12	
build	03-Dec-2025 16:10:12	> Task :releasesTemplates
build	03-Dec-2025 16:10:12	Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons:
build	03-Dec-2025 16:10:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:12	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:12	Stripping rc/test/etc for 2_11_5_1
build	03-Dec-2025 16:10:12	Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1/help/markdown/whatsnew/whatsnew-2_11_5_1.md
build	03-Dec-2025 16:10:12	
build	03-Dec-2025 16:10:12	> Task :prepare
build	03-Dec-2025 16:10:14	
build	03-Dec-2025 16:10:14	> Task :compileJava
build	03-Dec-2025 16:10:14	Setting target compatibility to 11
build	03-Dec-2025 16:10:21	
build	03-Dec-2025 16:10:21	> Task :processResources
build	03-Dec-2025 16:10:21	Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons:
build	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:21	
build	03-Dec-2025 16:10:21	> Task :classes
error	03-Dec-2025 16:10:21	Note: Some input files use or override a deprecated API.
error	03-Dec-2025 16:10:21	Note: Recompile with -Xlint:deprecation for details.
error	03-Dec-2025 16:10:21	Note: Some input files use unchecked or unsafe operations.
error	03-Dec-2025 16:10:21	Note: Recompile with -Xlint:unchecked for details.
build	03-Dec-2025 16:10:23	
build	03-Dec-2025 16:10:23	> Task :compileLinkCheck
build	03-Dec-2025 16:10:23	Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons:
build	03-Dec-2025 16:10:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:23	  - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-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	03-Dec-2025 16:10:25	
build	03-Dec-2025 16:10:25	> Task :linkCheck
build	03-Dec-2025 16:10:25	Checking help file links
build	03-Dec-2025 16:12:30	
build	03-Dec-2025 16:12:30	Results:
build	03-Dec-2025 16:12:30	161 distinct help targets
build	03-Dec-2025 16:12:30	161 help mappings
build	03-Dec-2025 16:12:30	0 invalid targets
build	03-Dec-2025 16:12:30	31 unused targets
build	03-Dec-2025 16:12:30	    uniprotfetcher: html/features/uniprotsequencefetcher.html
build	03-Dec-2025 16:12:30	    overviewprefs: html/features/preferences.html#overview
build	03-Dec-2025 16:12:30	    cdnafeatures: html/features/codingfeatures.html
build	03-Dec-2025 16:12:30	    startupprefs: html/features/preferences.html#startup
build	03-Dec-2025 16:12:30	    ensemblfetch: html/features/ensemblsequencefetcher.html
build	03-Dec-2025 16:12:30	    io.modellerpir: html/io/modellerpir.html
build	03-Dec-2025 16:12:30	    structureandpaefromfile: html/features/structurechooser.html#loadfromfile
build	03-Dec-2025 16:12:30	    pdbmcviewer: html/features/pdbviewer.html
build	03-Dec-2025 16:12:30	    groovy.colours: html/features/groovy.html#groovyColours
build	03-Dec-2025 16:12:30	    seqmappings: html/features/seqmappings.html
build	03-Dec-2025 16:12:30	    uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
build	03-Dec-2025 16:12:30	    splitframe.mirrorfonts: html/features/splitView.html#mirror
build	03-Dec-2025 16:12:30	    subtMatrices.pam250: html/calculations/scorematrices.html#pam250
build	03-Dec-2025 16:12:30	    search: html/features/search.html
build	03-Dec-2025 16:12:30	    viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
build	03-Dec-2025 16:12:30	    alformats: html/io/fileformats.html
build	03-Dec-2025 16:12:30	    strucprefs: html/features/preferences.html#structure
build	03-Dec-2025 16:12:30	    siftsmapping: html/features/siftsmapping.html
build	03-Dec-2025 16:12:30	    chimera.annotxfer: html/features/chimera.html#annotxfer
build	03-Dec-2025 16:12:30	    pdbfts: html/features/pdbsequencefetcher.html#pdbfts
build	03-Dec-2025 16:12:30	    newkeys: html/features/newkeystrokes.html
build	03-Dec-2025 16:12:30	    importvcf.attribs: html/features/importvcf.html#attribs
build	03-Dec-2025 16:12:30	    seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
build	03-Dec-2025 16:12:30	    structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch
build	03-Dec-2025 16:12:30	    jalarchive: html/features/jalarchive.html
build	03-Dec-2025 16:12:30	    newsreader: html/webServices/newsreader.html
build	03-Dec-2025 16:12:30	    jalviewcltool: html/features/commandline.html#script
build	03-Dec-2025 16:12:30	    popMenuAddref: html/menus/popupMenu.html#addrefannot
build	03-Dec-2025 16:12:30	    splitframe.virtualfeats: html/features/splitView.html#virtualfeats
build	03-Dec-2025 16:12:30	    paematrixformat: html/io/paematrixformat.html
build	03-Dec-2025 16:12:30	    overview: html/features/overview.html
build	03-Dec-2025 16:12:30	0 invalid map urls
build	03-Dec-2025 16:12:30	0 invalid image attributes
build	03-Dec-2025 16:12:30	520 internal href links (120 with anchors)
build	03-Dec-2025 16:12:30	0 invalid internal href links
build	03-Dec-2025 16:12:30	0 invalid internal anchor links
build	03-Dec-2025 16:12:30	112 external href links
build	03-Dec-2025 16:12:30	External links not verified as internet not available
build	03-Dec-2025 16:12:30	*** Success ***
build	03-Dec-2025 16:12:31	
build	03-Dec-2025 16:12:31	> Task :jar
build	03-Dec-2025 16:12:32	> Task :syncJars
build	03-Dec-2025 16:12:32	> Task :makeDist
build	03-Dec-2025 16:12:32	> Task :getdownWebsiteBuild
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	> Task :getdownDigest
build	03-Dec-2025 16:12:34	Generating digest file './build/website/docroot/getdown/default/11/digest.txt'...
error	03-Dec-2025 16:12:34	2025/12/03 16:12:32:845 WARNING Starting without install4j classes
error	03-Dec-2025 16:12:34	2025/12/03 16:12:33:463 WARNING Starting without install4j classes
build	03-Dec-2025 16:12:34	Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'...
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	> Task :getdown
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0.
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness.
build	03-Dec-2025 16:12:34	Please consult deprecation warnings for more details.
build	03-Dec-2025 16:12:34	
build	03-Dec-2025 16:12:34	BUILD SUCCESSFUL in 2m 27s
build	03-Dec-2025 16:12:34	21 actionable tasks: 21 executed
simple	03-Dec-2025 16:12:34	Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success
simple	03-Dec-2025 16:12:34	Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script'
command	03-Dec-2025 16:12:34	Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job #2 (JB-GDL93-JOB1-2)'\n ... running command line: \n/srv/bamboo/bamboo-home/temp/JB-GDL93-JOB1-2-ScriptBuildTask-4893570323285040820.sh\n ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\n ... using extra environment variables: \nbamboo_planRepository_1_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_dependency_parent_0=JB-GDB733-4\nbamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr\nbamboo_dependency_parent_total=1\nbamboo_planRepository_1_branchDisplayName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_repository_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL93-JOB1-2\nbamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL93-JOB1\nbamboo_planRepository_1_name=Jalview Gitlab\nbamboo_buildKey=JB-GDL93-JOB1\nbamboo_shortPlanName=bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_name=Jalview Gitlab\nbamboo_repository_46498486_previous_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_buildNumber=2\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-GDL93-JOB1-2\nbamboo_repository_46498486_revision_number=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_agentId=196609\nbamboo_planName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence\nbamboo_shortPlanKey=GDL93\nbamboo_shortJobKey=JOB1\nbamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk\nbamboo_planRepository_revision=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_buildTimeStamp=2025-12-03T16:10:04.058Z\nbamboo_repository_previous_revision_number=0ef8e143ad499423fa6af90141b658fb19c976ba\nbamboo_repository_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildResultKey=JB-GDL93-JOB1-2\nbamboo_repository_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - bug-JAL-4603_Export_files_missing_part_of_sequence - Default Job\nbamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11\nbamboo_planRepository_1_revision=db868848b73d9a08f5ee1b08a269436a41323446\nbamboo_CHANNEL=DEVELOP\nbamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant\nbamboo_repository_46498486_git_username=\nbamboo_repository_46498486_branch_name=bug/JAL-4603_Export_files_missing_part_of_sequence\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-GDL93 -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-4603_Export_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_files_missing_part_of_sequence\nbamboo_repository_46498486_git_branch=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_planRepository_1_type=gitv2\nbamboo_planRepository_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\nbamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11\nbamboo_capability_system_builderivy_Ivy=/usr\nbamboo_plan_storageTag=plan-46302543\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=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_repository_46498486_name=Jalview Gitlab\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-GDL93-JOB1\nbamboo_planKey=JB-GDL93\nbamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_username=\nbamboo_repository_46498486_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git\nbamboo_planRepository_1_branchName=bug/JAL-4603_Export_files_missing_part_of_sequence\n
simple	03-Dec-2025 16:12:34	Finished task 'Copy JVL file and produce link in HTML' with result: Success
simple	03-Dec-2025 16:12:34	Running post build plugin 'NCover Results Collector'
simple	03-Dec-2025 16:12:34	Running post build plugin 'Artifact Copier'
simple	03-Dec-2025 16:12:34	Publishing an artifact: getdown
simple	03-Dec-2025 16:12:34	Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 124.3 ms
simple	03-Dec-2025 16:12:34	Running post build plugin 'Artifactory Release Management Staging'
simple	03-Dec-2025 16:12:34	Running post build plugin 'Artifactory Build Info Copier'
simple	03-Dec-2025 16:12:34	Running post build plugin 'Artifactory Gradle Properties Info Copier'
simple	03-Dec-2025 16:12:35	Running post build plugin 'npm Cache Cleanup'
simple	03-Dec-2025 16:12:35	Running post build plugin 'Clover Results Collector'
simple	03-Dec-2025 16:12:35	Running post build plugin 'Docker Container Cleanup'
simple	03-Dec-2025 16:12:35	Finalising the build...
simple	03-Dec-2025 16:12:35	Stopping timer.
simple	03-Dec-2025 16:12:35	Build JB-GDL93-JOB1-2 completed.
simple	03-Dec-2025 16:12:35	Running on server: post build plugin 'NCover Results Collector'
simple	03-Dec-2025 16:12:35	Running on server: post build plugin 'Build Hanging Detection Configuration'
simple	03-Dec-2025 16:12:35	Running on server: post build plugin 'Clover Delta Calculator'
simple	03-Dec-2025 16:12:35	Running on server: post build plugin 'Maven Dependencies Postprocessor'
simple	03-Dec-2025 16:12:35	All post build plugins have finished
simple	03-Dec-2025 16:12:35	Generating build results summary...
simple	03-Dec-2025 16:12:35	Saving build results to disk...
simple	03-Dec-2025 16:12:35	Logging substituted variables...
simple	03-Dec-2025 16:12:35	Indexing build results...
simple	03-Dec-2025 16:12:35	Finished building JB-GDL93-JOB1-2.