Build: #3 was successful
Job: Clover and Tests was successful
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| 27-Nov-2025 17:21:20 | Build Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3) started building on agent Default Agent |
| 27-Nov-2025 17:21:20 | |
| 27-Nov-2025 17:21:20 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 |
| 27-Nov-2025 17:21:20 | Executing build Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3) |
| 27-Nov-2025 17:21:20 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 27-Nov-2025 17:21:20 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 |
| 27-Nov-2025 17:21:20 | Updating source code to revision: c0746f1378bd64b7cf72b082eca210d21f86feff |
| 27-Nov-2025 17:21:21 | Fetching 'refs/heads/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' from 'https://gitlab.jalview.org/jalview/jalview.git'. |
| 27-Nov-2025 17:21:23 | Checking out revision c0746f1378bd64b7cf72b082eca210d21f86feff. |
| 27-Nov-2025 17:21:23 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/62ce6c67e11163a982952b2962d6d7b0872110f0 |
| 27-Nov-2025 17:21:23 | d92ec98..c0746f1 bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest -> origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest |
| 27-Nov-2025 17:21:23 | * [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 |
| 27-Nov-2025 17:21:23 | b0fd08a..d96cd12 development/Release_2_11_5_Branch -> origin/development/Release_2_11_5_Branch |
| 27-Nov-2025 17:21:23 | * [new branch] patch/JAL-4601_stk_ss_annots_showhide -> origin/patch/JAL-4601_stk_ss_annots_showhide |
| 27-Nov-2025 17:21:23 | 86d2c84..a66e20b releases/Release_2_11_5_Branch -> origin/releases/Release_2_11_5_Branch |
| 27-Nov-2025 17:21:23 | Already on 'bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' |
| 27-Nov-2025 17:21:23 | Your branch is behind 'origin/bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest' by 1 commit, and can be fast-forwarded. |
| 27-Nov-2025 17:21:23 | (use "git pull" to update your local branch) |
| 27-Nov-2025 17:21:23 | HEAD is now at c0746f1 JAL-4581. Added an MD5 hash for jalview.ext.htsjdk.HtsContigDb. Made jalview.util.DigestUtils for MD5 and SHA256 digest. Adapted net.meyfa.sha256.Sha256 to not use java.nio.IntBuffer and java.nio.ByteBuffer (not supported by SwingJS). |
| 27-Nov-2025 17:21:23 | Updated source code to revision: c0746f1378bd64b7cf72b082eca210d21f86feff |
| 27-Nov-2025 17:21:23 | Finished task 'Checkout Default Repository' with result: Success |
| 27-Nov-2025 17:21:23 | Running pre-build action: VCS Version Collector |
| 27-Nov-2025 17:21:23 | Running pre-build action: Artifactory Release Staging |
| 27-Nov-2025 17:21:23 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 27-Nov-2025 17:21:23 | Bamboo Artifactory Plugin version: 2.6.2 |
| 27-Nov-2025 17:21:23 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3 bamboo_repository_46498584_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB727-JOB1 bamboo_repository_46498584_git_username= bamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_planRepository_name=Jalview Gitlab bamboo_repository_46498584_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97 LOGNAME=bamboo bamboo_buildNumber=3 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - 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| 27-Nov-2025 17:21:23 | 444 |
| 27-Nov-2025 17:21:25 | |
| 27-Nov-2025 17:21:25 | > Configure project : |
| 27-Nov-2025 17:21:25 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 27-Nov-2025 17:21:25 | JALVIEW_VERSION is set to '2.11.5.1' |
| 27-Nov-2025 17:21:25 | HEADLESS BUILD |
| 27-Nov-2025 17:21:25 | J2S ENABLED |
| 27-Nov-2025 17:21:25 | Using a LOCAL profile. |
| 27-Nov-2025 17:21:25 | eclipseDir exists |
| 27-Nov-2025 17:21:25 | |
| 27-Nov-2025 17:21:25 | > Task :clean |
| 27-Nov-2025 17:21:25 | > Task :cleanClover |
| 27-Nov-2025 17:21:25 | > Task :cleanTest UP-TO-DATE |
| 27-Nov-2025 17:21:28 | |
| 27-Nov-2025 17:21:28 | > Task :cloverInstrJava |
| 27-Nov-2025 17:21:28 | Clover: About to instrument 1108 files |
| 27-Nov-2025 17:21:28 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 27-Nov-2025 17:21:28 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover.db'. |
| 27-Nov-2025 17:21:28 | Processing files at 1.9 source level. |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:31 | WARN: Trying to add a statement but current method is null. Did you put CLOVER:OFF before a method signature and CLOVER:ON inside a method body? |
| 27-Nov-2025 17:21:40 | Clover all over. Instrumented 1108 files (113 packages). |
| 27-Nov-2025 17:21:42 | |
| 27-Nov-2025 17:21:42 | > Task :cloverInstrTests |
| 27-Nov-2025 17:21:42 | Clover: About to instrument test files |
| 27-Nov-2025 17:21:42 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 27-Nov-2025 17:21:42 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover.db'. |
| 27-Nov-2025 17:21:42 | Processing files at 1.9 source level. |
| 27-Nov-2025 17:21:45 | Clover all over. Instrumented 293 files (52 packages). |
| 27-Nov-2025 17:21:45 | 1619 test methods detected. |
| 27-Nov-2025 17:21:45 | |
| 27-Nov-2025 17:21:45 | > Task :cloverInstr |
| 27-Nov-2025 17:21:47 | |
| 27-Nov-2025 17:21:47 | > Task :compileCloverJava |
| 27-Nov-2025 17:21:47 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:21:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrJava' uses this output of task ':compileCloverJava' 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. |
| 27-Nov-2025 17:21:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes'. Reason: Task ':cloverInstrTests' uses this output of task ':compileCloverJava' 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. |
| 27-Nov-2025 17:21:47 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-instr'. Reason: Task ':compileCloverJava' uses this output of task ':cloverInstrJava' 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. |
| 27-Nov-2025 17:21:47 | Setting target compatibility to 11 |
| 27-Nov-2025 17:22:04 | Note: Some input files use or override a deprecated API. |
| 27-Nov-2025 17:22:04 | Note: Recompile with -Xlint:deprecation for details. |
| 27-Nov-2025 17:22:04 | Note: Some input files use unchecked or unsafe operations. |
| 27-Nov-2025 17:22:04 | Note: Recompile with -Xlint:unchecked for details. |
| 27-Nov-2025 17:22:11 | |
| 27-Nov-2025 17:22:11 | > Task :processCloverResources NO-SOURCE |
| 27-Nov-2025 17:22:11 | > Task :cloverClasses |
| 27-Nov-2025 17:22:11 | > Task :copyHelp |
| 27-Nov-2025 17:22:12 | > Task :buildIndices |
| 27-Nov-2025 17:22:12 | > Task :copyResources |
| 27-Nov-2025 17:22:13 | > Task :copyChannelResources |
| 27-Nov-2025 17:22:13 | |
| 27-Nov-2025 17:22:13 | > Task :createBuildProperties |
| 27-Nov-2025 17:22:13 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:22:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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. |
| 27-Nov-2025 17:22:13 | |
| 27-Nov-2025 17:22:13 | > Task :buildResources |
| 27-Nov-2025 17:22:13 | > Task :copyDocs |
| 27-Nov-2025 17:22:13 | |
| 27-Nov-2025 17:22:13 | > Task :convertMdFiles |
| 27-Nov-2025 17:22:13 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 27-Nov-2025 17:22:13 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 27-Nov-2025 17:22:13 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 27-Nov-2025 17:22:13 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/building.html |
| 27-Nov-2025 17:22:13 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 27-Nov-2025 17:22:13 | |
| 27-Nov-2025 17:22:13 | > Task :releasesTemplates |
| 27-Nov-2025 17:22:13 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:22:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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. |
| 27-Nov-2025 17:22:13 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-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. |
| 27-Nov-2025 17:22:13 | Stripping rc/test/etc for TEST |
| 27-Nov-2025 17:22:13 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 27-Nov-2025 17:22:13 | |
| 27-Nov-2025 17:22:13 | > Task :prepare |
| 27-Nov-2025 17:22:15 | |
| 27-Nov-2025 17:22:15 | > Task :compileJava |
| 27-Nov-2025 17:22:15 | Setting target compatibility to 11 |
| 27-Nov-2025 17:22:21 | Note: Some input files use or override a deprecated API. |
| 27-Nov-2025 17:22:21 | Note: Recompile with -Xlint:deprecation for details. |
| 27-Nov-2025 17:22:21 | Note: Some input files use unchecked or unsafe operations. |
| 27-Nov-2025 17:22:21 | Note: Recompile with -Xlint:unchecked for details. |
| 27-Nov-2025 17:22:23 | |
| 27-Nov-2025 17:22:23 | > Task :compileTestJava |
| 27-Nov-2025 17:22:23 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:22:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes'. Reason: Task ':compileTestJava' uses this output of task ':compileCloverJava' 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. |
| 27-Nov-2025 17:22:23 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-test-instr'. Reason: Task ':compileTestJava' uses this output of task ':cloverInstrTests' 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. |
| 27-Nov-2025 17:22:23 | Setting target compatibility to 11 |
| 27-Nov-2025 17:22:28 | Note: Some input files use or override a deprecated API. |
| 27-Nov-2025 17:22:28 | Note: Recompile with -Xlint:deprecation for details. |
| 27-Nov-2025 17:22:28 | Note: Some input files use unchecked or unsafe operations. |
| 27-Nov-2025 17:22:28 | Note: Recompile with -Xlint:unchecked for details. |
| 27-Nov-2025 17:22:31 | |
| 27-Nov-2025 17:22:31 | > Task :processTestResources |
| 27-Nov-2025 17:22:31 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/doc_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/help_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/resources/resources_build'. Reason: Task ':processTestResources' 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. |
| 27-Nov-2025 17:22:31 | |
| 27-Nov-2025 17:22:31 | > Task :testClasses |
| 27-Nov-2025 17:22:32 | |
| 27-Nov-2025 17:22:32 | > Task :testTask0 |
| 27-Nov-2025 17:22:32 | Running tests WITH clover |
| 27-Nov-2025 17:22:35 | WARNING: An illegal reflective access operation has occurred |
| 27-Nov-2025 17:22:35 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 27-Nov-2025 17:22:35 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 27-Nov-2025 17:22:35 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 27-Nov-2025 17:22:35 | WARNING: All illegal access operations will be denied in a future release |
| 27-Nov-2025 17:27:17 | |
| 27-Nov-2025 17:27:17 | > Task :testTask1 |
| 27-Nov-2025 17:27:17 | Running tests WITH clover |
| 27-Nov-2025 17:27:19 | WARNING: An illegal reflective access operation has occurred |
| 27-Nov-2025 17:27:19 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 27-Nov-2025 17:27:19 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 27-Nov-2025 17:27:19 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 27-Nov-2025 17:27:19 | WARNING: All illegal access operations will be denied in a future release |
| 27-Nov-2025 17:29:57 | |
| 27-Nov-2025 17:29:57 | > Task :testTask2 |
| 27-Nov-2025 17:29:57 | Running tests WITH clover |
| 27-Nov-2025 17:30:01 | |
| 27-Nov-2025 17:30:01 | > Task :testTask3 |
| 27-Nov-2025 17:30:01 | Running tests WITH clover |
| 27-Nov-2025 17:30:04 | WARNING: An illegal reflective access operation has occurred |
| 27-Nov-2025 17:30:04 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 27-Nov-2025 17:30:04 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 27-Nov-2025 17:30:04 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 27-Nov-2025 17:30:04 | WARNING: All illegal access operations will be denied in a future release |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | > Task :test NO-SOURCE |
| 27-Nov-2025 17:31:05 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 27-Nov-2025 17:31:05 | │jalview:testTask0 results: SUCCESS (1824 tests, 1824 successes, 0 failures, 0 skipped) in 4 minutes, 44.674 seconds │ |
| 27-Nov-2025 17:31:05 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask0/index.html│ |
| 27-Nov-2025 17:31:05 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 27-Nov-2025 17:31:05 | │jalview:testTask1 results: SUCCESS (62 tests, 62 successes, 0 failures, 0 skipped) in 2 minutes, 39.682 seconds │ |
| 27-Nov-2025 17:31:05 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask1/index.html│ |
| 27-Nov-2025 17:31:05 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 27-Nov-2025 17:31:05 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 4.052 seconds │ |
| 27-Nov-2025 17:31:05 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask2/index.html│ |
| 27-Nov-2025 17:31:05 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 27-Nov-2025 17:31:05 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 1 minutes, 5.701 seconds │ |
| 27-Nov-2025 17:31:05 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/testTask3/index.html│ |
| 27-Nov-2025 17:31:05 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 27-Nov-2025 17:31:05 | │OVERALL: results: SUCCESS (1912 tests, 1912 successes, 0 failures, 0 skipped) in 7 minutes, 94.109 seconds │ |
| 27-Nov-2025 17:31:05 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 27-Nov-2025 17:31:05 | Please consult deprecation warnings for more details. |
| 27-Nov-2025 17:31:05 | |
| 27-Nov-2025 17:31:05 | BUILD SUCCESSFUL in 9m 41s |
| 27-Nov-2025 17:31:05 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 27-Nov-2025 17:31:05 | Finished task 'Run tests with openclover under gradle' with result: Success |
| 27-Nov-2025 17:31:05 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 27-Nov-2025 17:31:05 | Bamboo Artifactory Plugin version: 2.6.2 |
| 27-Nov-2025 17:31:05 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests #3 (JB-GDB727-JOB1-3)' ... running command line: /home/bamboo/buildtools/x11-gradle/bin/gradle --no-daemon -Pclover=true -PJAVA_VERSION=11 cloverReport ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3 bamboo_repository_46498584_revision_number=c0746f1378bd64b7cf72b082eca210d21f86feff JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 bamboo_planRepository_1_name=Jalview Gitlab bamboo_buildKey=JB-GDB727-JOB1 bamboo_repository_46498584_git_username= bamboo_shortPlanName=bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_planRepository_name=Jalview Gitlab bamboo_repository_46498584_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97 LOGNAME=bamboo bamboo_buildNumber=3 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_shortJobName=Clover and Tests bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDB727-JOB1-3 bamboo_planRepository_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_46498584_name=Jalview Gitlab bamboo_shortPlanKey=GDB727 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=c0746f1378bd64b7cf72b082eca210d21f86feff bamboo_buildTimeStamp=2025-11-27T17:14:12.825Z bamboo_repository_previous_revision_number=d92ec98a32dc75a9fd0c635c803d00d60ce92f97 bamboo_planRepository_previousRevision=d92ec98a32dc75a9fd0c635c803d00d60ce92f97 bamboo_repository_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildResultKey=JB-GDB727-JOB1-3 bamboo_repository_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - bug-JAL-4581_jalviewjs_support_for_java_security_messagedigest - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_repository_46498584_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_1_revision=c0746f1378bd64b7cf72b082eca210d21f86feff SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Gitlab bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/x11-gradle/bin/gradle -Pclover=true -PJAVA_VERSION=11 -Ptestng_excluded_groups=Not-bamboo clean cleanTest test JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_jobFailed=false bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=d92ec98a32dc75a9fd0c635c803d00d60ce92f97 bamboo_planRepository_branchDisplayName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46302739 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_repository_git_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1 bamboo_planKey=JB-GDB727 bamboo_planRepository_1_repositoryUrl=https://gitlab.jalview.org/jalview/jalview.git bamboo_planRepository_username= bamboo_repository_46498584_branch_name=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest bamboo_repository_46498584_git_branch=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest HOME=/home/bamboo bamboo_planRepository_1_branchName=bug/JAL-4581_jalviewjs_support_for_java_security_messagedigest PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 27-Nov-2025 17:31:05 | 444 |
| 27-Nov-2025 17:31:12 | |
| 27-Nov-2025 17:31:12 | > Configure project : |
| 27-Nov-2025 17:31:12 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 27-Nov-2025 17:31:12 | JALVIEW_VERSION is set to '2.11.5.1' |
| 27-Nov-2025 17:31:12 | HEADLESS BUILD |
| 27-Nov-2025 17:31:12 | J2S ENABLED |
| 27-Nov-2025 17:31:13 | Using a LOCAL profile. |
| 27-Nov-2025 17:31:15 | eclipseDir exists |
| 27-Nov-2025 17:31:17 | |
| 27-Nov-2025 17:31:17 | > Task :cloverHtmlReport |
| 27-Nov-2025 17:31:17 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 27-Nov-2025 17:31:18 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/clover' |
| 27-Nov-2025 17:32:06 | ERROR: Invalid Java source found or Clover failed to parse it: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/src/jalview/schemes/ResidueProperties.java |
| 27-Nov-2025 17:32:13 | Done. Processed 117 packages in 54563ms (466ms per package). |
| 27-Nov-2025 17:32:21 | |
| 27-Nov-2025 17:32:21 | > Task :cloverXmlReport |
| 27-Nov-2025 17:32:21 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 27-Nov-2025 17:32:25 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/clover/clover.xml' |
| 27-Nov-2025 17:32:25 | |
| 27-Nov-2025 17:32:25 | > Task :cloverReport |
| 27-Nov-2025 17:32:25 | |
| 27-Nov-2025 17:32:25 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 27-Nov-2025 17:32:25 | |
| 27-Nov-2025 17:32:25 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 27-Nov-2025 17:32:25 | |
| 27-Nov-2025 17:32:25 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 27-Nov-2025 17:32:25 | |
| 27-Nov-2025 17:32:25 | BUILD SUCCESSFUL in 1m 19s |
| 27-Nov-2025 17:32:25 | 2 actionable tasks: 2 executed |
| 27-Nov-2025 17:32:25 | Finished task 'Clover Report' with result: Success |
| 27-Nov-2025 17:32:25 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 27-Nov-2025 17:32:25 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1... |
| 27-Nov-2025 17:32:26 | Finished task 'TestNG Parser' with result: Success |
| 27-Nov-2025 17:32:26 | Running post build plugin 'NCover Results Collector' |
| 27-Nov-2025 17:32:26 | Running post build plugin 'Artifact Copier' |
| 27-Nov-2025 17:32:26 | Publishing an artifact: Clover Report (System) |
| 27-Nov-2025 17:32:31 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 5.878 s |
| 27-Nov-2025 17:32:31 | Publishing an artifact: TestNG report |
| 27-Nov-2025 17:32:31 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB727-JOB1/build/reports/tests/test does not exist. |
| 27-Nov-2025 17:32:31 | The artifact hasn't been successfully published after 4.337 ms |
| 27-Nov-2025 17:32:31 | Running post build plugin 'Artifactory Release Management Staging' |
| 27-Nov-2025 17:32:31 | Running post build plugin 'Artifactory Build Info Copier' |
| 27-Nov-2025 17:32:31 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 27-Nov-2025 17:32:31 | Running post build plugin 'npm Cache Cleanup' |
| 27-Nov-2025 17:32:31 | Running post build plugin 'Clover Results Collector' |
| 27-Nov-2025 17:32:31 | Running post build plugin 'Docker Container Cleanup' |
| 27-Nov-2025 17:32:31 | Finalising the build... |
| 27-Nov-2025 17:32:31 | Stopping timer. |
| 27-Nov-2025 17:32:31 | Build JB-GDB727-JOB1-3 completed. |
| 27-Nov-2025 17:32:31 | Running on server: post build plugin 'NCover Results Collector' |
| 27-Nov-2025 17:32:31 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 27-Nov-2025 17:32:31 | Running on server: post build plugin 'Clover Delta Calculator' |
| 27-Nov-2025 17:32:31 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 27-Nov-2025 17:32:31 | All post build plugins have finished |
| 27-Nov-2025 17:32:31 | Generating build results summary... |
| 27-Nov-2025 17:32:32 | Saving build results to disk... |
| 27-Nov-2025 17:32:32 | Logging substituted variables... |
| 27-Nov-2025 17:32:32 | Indexing build results... |
| 27-Nov-2025 17:32:32 | Finished building JB-GDB727-JOB1-3. |