Build: #9 was successful
Job: Clover and Tests was successful
Build log
The build generated 248 lines of output. Download or view full build log
| 06-Dec-2024 13:47:00 | Build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9) started building on agent Default Agent |
| 06-Dec-2024 13:47:00 | |
| 06-Dec-2024 13:47:00 | Build working directory is /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 |
| 06-Dec-2024 13:47:00 | Executing build Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9) |
| 06-Dec-2024 13:47:00 | Starting task 'Checkout Default Repository' of type 'com.atlassian.bamboo.plugins.vcs:task.vcs.checkout' |
| 06-Dec-2024 13:47:00 | Checking out into /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1 |
| 06-Dec-2024 13:47:00 | Updating source code to revision: 39291a3fa3b81f3a82111b067ffd51c87b14fe8d |
| 06-Dec-2024 13:47:00 | Fetching 'refs/heads/feature/JAL-4386_JAL-4435_reformat_node_labels' from 'http://source.jalview.org/git/jalview.git'. |
| 06-Dec-2024 13:47:00 | Checking out revision 39291a3fa3b81f3a82111b067ffd51c87b14fe8d. |
| 06-Dec-2024 13:47:00 | From file:///srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache/2597b807d50ab756c763be1d374b09c84289a164 |
| 06-Dec-2024 13:47:00 | c8ec18c..39291a3 feature/JAL-4386_JAL-4435_reformat_node_labels -> origin/feature/JAL-4386_JAL-4435_reformat_node_labels |
| 06-Dec-2024 13:47:00 | Already on 'feature/JAL-4386_JAL-4435_reformat_node_labels' |
| 06-Dec-2024 13:47:00 | Your branch is behind 'origin/feature/JAL-4386_JAL-4435_reformat_node_labels' by 1 commit, and can be fast-forwarded. |
| 06-Dec-2024 13:47:00 | (use "git pull" to update your local branch) |
| 06-Dec-2024 13:47:00 | HEAD is now at 39291a3 JAL-4435 Corrections on coloured line visualisation |
| 06-Dec-2024 13:47:00 | Updated source code to revision: 39291a3fa3b81f3a82111b067ffd51c87b14fe8d |
| 06-Dec-2024 13:47:00 | Finished task 'Checkout Default Repository' with result: Success |
| 06-Dec-2024 13:47:00 | Running pre-build action: VCS Version Collector |
| 06-Dec-2024 13:47:00 | Running pre-build action: Artifactory Release Staging |
| 06-Dec-2024 13:47:00 | Starting task 'Run tests with openclover under gradle' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 06-Dec-2024 13:47:00 | Bamboo Artifactory Plugin version: 2.6.2 |
| 06-Dec-2024 13:47:00 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9)' ... 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-GDB633-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_repository_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-9 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-GDB633-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB633-JOB1 bamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels bamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_repository_46498136_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d bamboo_buildNumber=9 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-GDB633-JOB1-9 bamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - 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| 06-Dec-2024 13:47:00 | 444 |
| 06-Dec-2024 13:47:01 | |
| 06-Dec-2024 13:47:01 | > Configure project : |
| 06-Dec-2024 13:47:01 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 06-Dec-2024 13:47:01 | JALVIEW_VERSION is set to '2.11.4.0' |
| 06-Dec-2024 13:47:01 | HEADLESS BUILD |
| 06-Dec-2024 13:47:01 | J2S ENABLED |
| 06-Dec-2024 13:47:01 | Using a LOCAL profile. |
| 06-Dec-2024 13:47:01 | eclipseDir exists |
| 06-Dec-2024 13:47:01 | |
| 06-Dec-2024 13:47:01 | > Task :clean |
| 06-Dec-2024 13:47:01 | > Task :cleanClover |
| 06-Dec-2024 13:47:01 | > Task :cleanTest UP-TO-DATE |
| 06-Dec-2024 13:47:04 | |
| 06-Dec-2024 13:47:04 | > Task :cloverInstrJava |
| 06-Dec-2024 13:47:04 | Clover: About to instrument 1102 files |
| 06-Dec-2024 13:47:04 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 06-Dec-2024 13:47:04 | Creating new database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. |
| 06-Dec-2024 13:47:04 | Processing files at 1.9 source level. |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:06 | 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? |
| 06-Dec-2024 13:47:13 | Clover all over. Instrumented 1102 files (111 packages). |
| 06-Dec-2024 13:47:15 | |
| 06-Dec-2024 13:47:15 | > Task :cloverInstrTests |
| 06-Dec-2024 13:47:15 | Clover: About to instrument test files |
| 06-Dec-2024 13:47:15 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 06-Dec-2024 13:47:15 | Updating existing database at '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover.db'. |
| 06-Dec-2024 13:47:15 | Processing files at 1.9 source level. |
| 06-Dec-2024 13:47:18 | Clover all over. Instrumented 290 files (52 packages). |
| 06-Dec-2024 13:47:18 | 1591 test methods detected. |
| 06-Dec-2024 13:47:18 | |
| 06-Dec-2024 13:47:18 | > Task :cloverInstr |
| 06-Dec-2024 13:47:20 | |
| 06-Dec-2024 13:47:20 | > Task :compileCloverJava |
| 06-Dec-2024 13:47:20 | Execution optimizations have been disabled for task ':compileCloverJava' to ensure correctness due to the following reasons: |
| 06-Dec-2024 13:47:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:20 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:20 | Setting target compatibility to 11 |
| 06-Dec-2024 13:47:32 | Note: Some input files use or override a deprecated API. |
| 06-Dec-2024 13:47:32 | Note: Recompile with -Xlint:deprecation for details. |
| 06-Dec-2024 13:47:32 | Note: Some input files use unchecked or unsafe operations. |
| 06-Dec-2024 13:47:32 | Note: Recompile with -Xlint:unchecked for details. |
| 06-Dec-2024 13:47:37 | |
| 06-Dec-2024 13:47:37 | > Task :processCloverResources NO-SOURCE |
| 06-Dec-2024 13:47:37 | > Task :cloverClasses |
| 06-Dec-2024 13:47:38 | > Task :copyHelp |
| 06-Dec-2024 13:47:39 | > Task :buildIndices |
| 06-Dec-2024 13:47:39 | > Task :copyResources |
| 06-Dec-2024 13:47:39 | > Task :copyChannelResources |
| 06-Dec-2024 13:47:39 | |
| 06-Dec-2024 13:47:39 | > Task :createBuildProperties |
| 06-Dec-2024 13:47:39 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 06-Dec-2024 13:47:39 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:39 | |
| 06-Dec-2024 13:47:39 | > Task :buildResources |
| 06-Dec-2024 13:47:39 | > Task :copyDocs |
| 06-Dec-2024 13:47:39 | |
| 06-Dec-2024 13:47:39 | > Task :convertMdFiles |
| 06-Dec-2024 13:47:39 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 06-Dec-2024 13:47:39 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 06-Dec-2024 13:47:39 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 06-Dec-2024 13:47:39 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/building.html |
| 06-Dec-2024 13:47:39 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 06-Dec-2024 13:47:40 | |
| 06-Dec-2024 13:47:40 | > Task :releasesTemplates |
| 06-Dec-2024 13:47:40 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 06-Dec-2024 13:47:40 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:40 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:40 | Stripping rc/test/etc for TEST |
| 06-Dec-2024 13:47:40 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/help/markdown/whatsnew/whatsnew-TEST.md |
| 06-Dec-2024 13:47:40 | |
| 06-Dec-2024 13:47:40 | > Task :prepare |
| 06-Dec-2024 13:47:42 | |
| 06-Dec-2024 13:47:42 | > Task :compileJava |
| 06-Dec-2024 13:47:42 | Setting target compatibility to 11 |
| 06-Dec-2024 13:47:47 | Note: Some input files use or override a deprecated API. |
| 06-Dec-2024 13:47:47 | Note: Recompile with -Xlint:deprecation for details. |
| 06-Dec-2024 13:47:47 | Note: Some input files use unchecked or unsafe operations. |
| 06-Dec-2024 13:47:47 | Note: Recompile with -Xlint:unchecked for details. |
| 06-Dec-2024 13:47:49 | |
| 06-Dec-2024 13:47:49 | > Task :compileTestJava |
| 06-Dec-2024 13:47:49 | Execution optimizations have been disabled for task ':compileTestJava' to ensure correctness due to the following reasons: |
| 06-Dec-2024 13:47:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:49 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:49 | Setting target compatibility to 11 |
| 06-Dec-2024 13:47:53 | Note: Some input files use or override a deprecated API. |
| 06-Dec-2024 13:47:53 | Note: Recompile with -Xlint:deprecation for details. |
| 06-Dec-2024 13:47:53 | Note: Some input files use unchecked or unsafe operations. |
| 06-Dec-2024 13:47:53 | Note: Recompile with -Xlint:unchecked for details. |
| 06-Dec-2024 13:47:54 | |
| 06-Dec-2024 13:47:54 | > Task :processTestResources |
| 06-Dec-2024 13:47:54 | Execution optimizations have been disabled for task ':processTestResources' to ensure correctness due to the following reasons: |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-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. |
| 06-Dec-2024 13:47:54 | |
| 06-Dec-2024 13:47:54 | > Task :testClasses |
| 06-Dec-2024 13:47:56 | |
| 06-Dec-2024 13:47:56 | > Task :testTask0 |
| 06-Dec-2024 13:47:56 | Running tests WITH clover |
| 06-Dec-2024 13:47:59 | WARNING: An illegal reflective access operation has occurred |
| 06-Dec-2024 13:47:59 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 06-Dec-2024 13:47:59 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 06-Dec-2024 13:47:59 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 06-Dec-2024 13:47:59 | WARNING: All illegal access operations will be denied in a future release |
| 06-Dec-2024 13:51:47 | |
| 06-Dec-2024 13:51:47 | > Task :testTask1 |
| 06-Dec-2024 13:51:47 | Running tests WITH clover |
| 06-Dec-2024 13:51:49 | WARNING: An illegal reflective access operation has occurred |
| 06-Dec-2024 13:51:49 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 06-Dec-2024 13:51:49 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 06-Dec-2024 13:51:49 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 06-Dec-2024 13:51:49 | WARNING: All illegal access operations will be denied in a future release |
| 06-Dec-2024 13:53:23 | |
| 06-Dec-2024 13:53:23 | > Task :testTask2 |
| 06-Dec-2024 13:53:23 | Running tests WITH clover |
| 06-Dec-2024 13:53:26 | |
| 06-Dec-2024 13:53:26 | > Task :testTask3 |
| 06-Dec-2024 13:53:26 | Running tests WITH clover |
| 06-Dec-2024 13:53:28 | WARNING: An illegal reflective access operation has occurred |
| 06-Dec-2024 13:53:28 | WARNING: Illegal reflective access by jalview.gui.Desktop (file:/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/clover/clover-classes/) to field sun.awt.X11.XToolkit.awtAppClassName |
| 06-Dec-2024 13:53:28 | WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop |
| 06-Dec-2024 13:53:28 | WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations |
| 06-Dec-2024 13:53:28 | WARNING: All illegal access operations will be denied in a future release |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | > Task :test NO-SOURCE |
| 06-Dec-2024 13:54:14 | ┌──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐ |
| 06-Dec-2024 13:54:14 | │jalview:testTask0 results: SUCCESS (1693 tests, 1693 successes, 0 failures, 0 skipped) in 3 minutes, 50.461 seconds │ |
| 06-Dec-2024 13:54:14 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask0/index.html│ |
| 06-Dec-2024 13:54:14 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 06-Dec-2024 13:54:14 | │jalview:testTask1 results: SUCCESS (49 tests, 49 successes, 0 failures, 0 skipped) in 1 minutes, 35.685 seconds │ |
| 06-Dec-2024 13:54:14 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask1/index.html│ |
| 06-Dec-2024 13:54:14 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 06-Dec-2024 13:54:14 | │jalview:testTask2 results: SUCCESS (1 tests, 1 successes, 0 failures, 0 skipped) in 3.411 seconds │ |
| 06-Dec-2024 13:54:14 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask2/index.html│ |
| 06-Dec-2024 13:54:14 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 06-Dec-2024 13:54:14 | │jalview:testTask3 results: SUCCESS (25 tests, 25 successes, 0 failures, 0 skipped) in 49.015 seconds │ |
| 06-Dec-2024 13:54:14 | │Report file: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/testTask3/index.html│ |
| 06-Dec-2024 13:54:14 | ├──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┤ |
| 06-Dec-2024 13:54:14 | │OVERALL: results: SUCCESS (1768 tests, 1768 successes, 0 failures, 0 skipped) in 4 minutes, 138.572 seconds │ |
| 06-Dec-2024 13:54:14 | └──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘ |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | Execution optimizations have been disabled for 5 invalid unit(s) of work during this build to ensure correctness. |
| 06-Dec-2024 13:54:14 | Please consult deprecation warnings for more details. |
| 06-Dec-2024 13:54:14 | |
| 06-Dec-2024 13:54:14 | BUILD SUCCESSFUL in 7m 13s |
| 06-Dec-2024 13:54:14 | 21 actionable tasks: 20 executed, 1 up-to-date |
| 06-Dec-2024 13:54:14 | Finished task 'Run tests with openclover under gradle' with result: Success |
| 06-Dec-2024 13:54:14 | Starting task 'Clover Report' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 06-Dec-2024 13:54:14 | Bamboo Artifactory Plugin version: 2.6.2 |
| 06-Dec-2024 13:54:14 | Beginning to execute external process for build 'Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests #9 (JB-GDB633-JOB1-9)' ... 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-GDB633-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_repository_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDB633-JOB1-9 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-GDB633-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDB633-JOB1 bamboo_shortPlanName=feature-JAL-4386_JAL-4435_reformat_node_labels bamboo_repository_46498136_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_repository_46498136_revision_number=39291a3fa3b81f3a82111b067ffd51c87b14fe8d bamboo_buildNumber=9 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-GDB633-JOB1-9 bamboo_repository_46498136_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_agentId=196609 bamboo_planName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels bamboo_shortPlanKey=GDB633 bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=39291a3fa3b81f3a82111b067ffd51c87b14fe8d bamboo_buildTimeStamp=2024-12-06T13:47:00.413Z bamboo_repository_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32 bamboo_planRepository_previousRevision=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32 bamboo_repository_git_branch=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_buildResultKey=JB-GDB633-JOB1-9 bamboo_repository_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_buildPlanName=Jalview Builds - Gradle Develop Build - feature-JAL-4386_JAL-4435_reformat_node_labels - Clover and Tests bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=39291a3fa3b81f3a82111b067ffd51c87b14fe8d SHLVL=1 bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git 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_repository_46498136_previous_revision_number=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=feature/JAL-4386_JAL-4435_reformat_node_labels 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=c8ec18cdaf58a232459fe4a2bc6fa2bb70678c32 bamboo_planRepository_branchDisplayName=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels bamboo_repository_46498136_branch_name=feature/JAL-4386_JAL-4435_reformat_node_labels _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_repository_46498136_git_username= bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301871 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=http://source.jalview.org/git/jalview.git bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_repository_46498136_name=Jalview Git 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-GDB633-JOB1 bamboo_planKey=JB-GDB633 bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=feature/JAL-4386_JAL-4435_reformat_node_labels PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 06-Dec-2024 13:54:14 | 444 |
| 06-Dec-2024 13:54:21 | |
| 06-Dec-2024 13:54:21 | > Configure project : |
| 06-Dec-2024 13:54:21 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 06-Dec-2024 13:54:21 | JALVIEW_VERSION is set to '2.11.4.0' |
| 06-Dec-2024 13:54:21 | HEADLESS BUILD |
| 06-Dec-2024 13:54:21 | J2S ENABLED |
| 06-Dec-2024 13:54:21 | Using a LOCAL profile. |
| 06-Dec-2024 13:54:22 | eclipseDir exists |
| 06-Dec-2024 13:54:24 | |
| 06-Dec-2024 13:54:24 | > Task :cloverHtmlReport |
| 06-Dec-2024 13:54:24 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 06-Dec-2024 13:54:25 | Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover' |
| 06-Dec-2024 13:55:03 | Done. Processed 115 packages in 37700ms (327ms per package). |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | > Task :cloverXmlReport |
| 06-Dec-2024 13:55:09 | OpenClover Version 4.4.1, built on October 11 2019 (build-1020) |
| 06-Dec-2024 13:55:09 | Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/clover/clover.xml' |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | > Task :cloverReport |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 06-Dec-2024 13:55:09 | |
| 06-Dec-2024 13:55:09 | BUILD SUCCESSFUL in 55s |
| 06-Dec-2024 13:55:09 | 2 actionable tasks: 2 executed |
| 06-Dec-2024 13:55:10 | Finished task 'Clover Report' with result: Success |
| 06-Dec-2024 13:55:10 | Starting task 'TestNG Parser' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng' |
| 06-Dec-2024 13:55:10 | Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1... |
| 06-Dec-2024 13:55:10 | Finished task 'TestNG Parser' with result: Success |
| 06-Dec-2024 13:55:10 | Running post build plugin 'NCover Results Collector' |
| 06-Dec-2024 13:55:10 | Running post build plugin 'Artifact Copier' |
| 06-Dec-2024 13:55:10 | Publishing an artifact: Clover Report (System) |
| 06-Dec-2024 13:55:11 | Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [build/reports/clover] in 1.468 s |
| 06-Dec-2024 13:55:11 | Publishing an artifact: TestNG report |
| 06-Dec-2024 13:55:11 | Unable to publish artifact [TestNG report]: the source directory /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDB633-JOB1/build/reports/tests/test does not exist. |
| 06-Dec-2024 13:55:11 | The artifact hasn't been successfully published after 1.339 ms |
| 06-Dec-2024 13:55:11 | Running post build plugin 'Artifactory Release Management Staging' |
| 06-Dec-2024 13:55:11 | Running post build plugin 'Artifactory Build Info Copier' |
| 06-Dec-2024 13:55:11 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 06-Dec-2024 13:55:11 | Running post build plugin 'npm Cache Cleanup' |
| 06-Dec-2024 13:55:11 | Running post build plugin 'Clover Results Collector' |
| 06-Dec-2024 13:55:11 | Running post build plugin 'Docker Container Cleanup' |
| 06-Dec-2024 13:55:11 | Finalising the build... |
| 06-Dec-2024 13:55:11 | Stopping timer. |
| 06-Dec-2024 13:55:11 | Build JB-GDB633-JOB1-9 completed. |
| 06-Dec-2024 13:55:11 | Running on server: post build plugin 'NCover Results Collector' |
| 06-Dec-2024 13:55:11 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 06-Dec-2024 13:55:11 | Running on server: post build plugin 'Clover Delta Calculator' |
| 06-Dec-2024 13:55:11 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 06-Dec-2024 13:55:11 | All post build plugins have finished |
| 06-Dec-2024 13:55:11 | Generating build results summary... |
| 06-Dec-2024 13:55:11 | Saving build results to disk... |
| 06-Dec-2024 13:55:11 | Logging substituted variables... |
| 06-Dec-2024 13:55:11 | Indexing build results... |
| 06-Dec-2024 13:55:11 | Finished building JB-GDB633-JOB1-9. |